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Cao W, Huang C, Zhou X, Zhou S, Deng Y. Engineering two-component systems for advanced biosensing: From architecture to applications in biotechnology. Biotechnol Adv 2024; 75:108404. [PMID: 39002783 DOI: 10.1016/j.biotechadv.2024.108404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/05/2024] [Accepted: 07/07/2024] [Indexed: 07/15/2024]
Abstract
Two-component systems (TCSs) are prevalent signaling pathways in bacteria. These systems mediate phosphotransfer between histidine kinase and a response regulator, facilitating responses to diverse physical, chemical, and biological stimuli. Advancements in synthetic and structural biology have repurposed TCSs for applications in monitoring heavy metals, disease-associated biomarkers, and the production of bioproducts. However, the utility of many TCS biosensors is hindered by undesired performance due to the lack of effective engineering methods. Here, we briefly discuss the architectures and regulatory mechanisms of TCSs. We also summarize the recent advancements in TCS engineering by experimental or computational-based methods to fine-tune the biosensor functional parameters, such as response curve and specificity. Engineered TCSs have great potential in the medical, environmental, and biorefinery fields, demonstrating a crucial role in a wide area of biotechnology.
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Affiliation(s)
- Wenyan Cao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Chao Huang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xuan Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Shenghu Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China.
| | - Yu Deng
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China.
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2
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Mondal S, Pandey D, Singh SP. Chromatic acclimation in cyanobacteria renders robust photosynthesis and fitness in dynamic light environment: Recent advances and future perspectives. PHYSIOLOGIA PLANTARUM 2024; 176:e14536. [PMID: 39323055 DOI: 10.1111/ppl.14536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/27/2024]
Abstract
Cyanobacteria are photoautotrophic organisms that use light and water as a source of energy and electrons, respectively, to fix atmospheric carbon dioxide and release oxygen as a by-product during photosynthesis. However, photosynthesis and fitness of organisms are challenged by seasonal and diurnal fluctuations in light environments. Also, the distribution of cyanobacteria in a water column is subject to changes in the light regime. The quality and quantity of light change significantly in low and bright light environments that either limit photochemistry or result in photoinhibition due to an excess amount of light reaching reaction centers. Therefore, cyanobacteria have to adjust their light-harvesting machinery and cell morphology for the optimal harvesting of light. This adjustment of light-harvesting involves remodeling of the light-harvesting complex called phycobilisome or incorporation of chlorophyll molecules such as chlorophyll d and f into their light-harvesting machinery. Thus, photoacclimation responses of cyanobacteria at the level of pigment composition and cell morphology maximize their photosynthetic ability and fitness under a dynamic light environment. Cyanobacteria exhibit different types of photoacclimation responses that are commonly known as chromatic acclimation (CA). In this work, we discuss different types of CA reported in cyanobacteria and present a molecular mechanism of well-known type 3 CA where phycoerythrin and phycocyanin of phycobilisome changes according to light signals. We also include other aspects of type 3 CA that have been recently studied at a molecular level and highlight the importance of morphogenes, cytoskeleton, and carboxysome proteins. In summary, CA gives a unique competitive benefit to cyanobacteria by increasing their resource utilization ability and fitness.
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Affiliation(s)
- Soumila Mondal
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Deepa Pandey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Shailendra P Singh
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
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3
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Kim C, Yun SR, Lee SJ, Kim SO, Lee H, Choi J, Kim JG, Kim TW, You S, Kosheleva I, Noh T, Baek J, Ihee H. Structural dynamics of protein-protein association involved in the light-induced transition of Avena sativa LOV2 protein. Nat Commun 2024; 15:6991. [PMID: 39143073 PMCID: PMC11324726 DOI: 10.1038/s41467-024-51461-z] [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: 02/05/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024] Open
Abstract
The Light-oxygen-voltage-sensing domain (LOV) superfamily, found in enzymes and signal transduction proteins, plays a crucial role in converting light signals into structural signals, mediating various biological mechanisms. While time-resolved spectroscopic studies have revealed the dynamics of the LOV-domain chromophore's electronic structures, understanding the structural changes in the protein moiety, particularly regarding light-induced dimerization, remains challenging. Here, we utilize time-resolved X-ray liquidography to capture the light-induced dimerization of Avena sativa LOV2. Our analysis unveils that dimerization occurs within milliseconds after the unfolding of the A'α and Jα helices in the microsecond time range. Notably, our findings suggest that protein-protein interactions (PPIs) among the β-scaffolds, mediated by helix unfolding, play a key role in dimerization. In this work, we offer structural insights into the dimerization of LOV2 proteins following structural changes in the A'α and Jα helices, as well as mechanistic insights into the protein-protein association process driven by PPIs.
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Affiliation(s)
- Changin Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - So Ri Yun
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Sang Jin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Seong Ok Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hyosub Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jungkweon Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Seyoung You
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL, 60637, USA
| | - Taeyoon Noh
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jonghoon Baek
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea.
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Cleere MM, Gardner KH. Optogenetic control of phosphate-responsive genes using single component fusion proteins in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.605841. [PMID: 39131330 PMCID: PMC11312615 DOI: 10.1101/2024.08.02.605841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Blue light illumination can be detected by Light-Oxygen-Voltage (LOV) photosensing proteins and translated into a range of biochemical responses, facilitating the generation of novel optogenetic tools to control cellular function. Here we develop new variants of our previously described VP-EL222 light-dependent transcription factor and apply them to study the phosphate-responsive signaling (PHO) pathway in the budding yeast Saccharomyces cerevisiae, exemplifying the utilities of these new tools. Focusing first on the VP-EL222 protein itself, we quantified the tunability of gene expression as a function of light intensity and duration, and demonstrated that this system can tolerate the addition of substantially larger effector domains without impacting function. We further demonstrated the utility of several EL222-driven transcriptional controllers in both plasmid and genomic settings, using the PHO5 and PHO84 promoters in their native chromosomal contexts as examples. These studies highlight the utility of light-controlled gene activation using EL222 tethered to either artificial transcription domains or yeast activator proteins (Pho4). Similarly, we demonstrate the ability to optogenetically repress gene expression with EL222 fused to the yeast Ume6 protein. We finally investigated the effects of moving EL222 recruitment sites to different locations within the PHO5 and PHO84 promoters, as well as determining how this artificial light-controlled regulation could be integrated with the native controls dependent on inorganic phosphate (Pi) availability. Taken together, our work expands the applicability of these versatile optogenetic tools in the types of functionality they can deliver and biological questions that can be probed.
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Affiliation(s)
- Matthew M Cleere
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY 10016
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Biochemistry, Chemistry, and Biology Ph.D. Programs, Graduate Center, City University of New York, New York, NY 10016
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
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Hernández-Herreros N, Rodríguez A, Galán B, Auxiliadora Prieto M. Boosting hydrogen production in Rhodospirillum rubrum by syngas-driven photoheterotrophic adaptive evolution. BIORESOURCE TECHNOLOGY 2024; 406:130972. [PMID: 38876276 DOI: 10.1016/j.biortech.2024.130972] [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: 03/16/2024] [Revised: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024]
Abstract
Rhodospirillum rubrum is a photosynthetic purple non-sulphur bacterium with great potential to be used for complex waste valorisation in biotechnological applications due to its metabolic versatility. This study investigates the production of hydrogen (H2) and polyhydroxyalkanoates (PHA) by R. rubrum from syngas under photoheterotrophic conditions. An adaptive laboratory evolution strategy (ALE) has been carried out to improve the yield of the process. After 200 generations, two evolved strains were selected that showed reduced lag phase and enhanced poly-3-hydroxybutyrate (PHB) and H2 synthesis compared to the parental strain. Genomic analysis of the photo-adapted (PA) variants showed four genes with single point mutations, including the photosynthesis gene expression regulator PpsR. The proteome of the variants suggested that the adapted variants overproduced H2 due to a more efficient CO oxidation through the CO-dehydrogenase enzyme complex and confirmed that energy acquisition was enhanced through overexpression of the photosynthetic system and metal cofactors essential for pigment biosynthesis.
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Affiliation(s)
- Natalia Hernández-Herreros
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Alberto Rodríguez
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Beatriz Galán
- Microbial & Plant Biotechnology Department, Environmental Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
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6
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Klepa MS, diCenzo GC, Hungria M. Comparative genomic analysis of Bradyrhizobium strains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions. Microbiol Spectr 2024; 12:e0026024. [PMID: 38842312 PMCID: PMC11218460 DOI: 10.1128/spectrum.00260-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 05/01/2024] [Indexed: 06/07/2024] Open
Abstract
Bradyrhizobium is known for fixing atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight natural variants of the parental strains, Bradyrhizobium japonicum SEMIA 586 (=CNPSo 17) or Bradyrhizobium diazoefficiens SEMIA 566 (=CNPSo 10). CNPSo 17 and CNPSo 10 were used as commercial inoculants for soybean crops in Brazil at the beginning of the crop expansion in the southern region in the 1960s-1970s. Variants derived from these parental strains were obtained in the late 1980s through a strain selection program aimed at identifying elite strains adapted to a new cropping frontier in the central-western Cerrado region, with a higher capacity of biological nitrogen fixation (BNF) and competitiveness. Here, we aimed to detect genetic variations possibly related to BNF, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains. The core genome phylogeny revealed that strains of each group are closely related, as confirmed by high average nucleotide identity values. However, variants accumulated divergences resulting from horizontal gene transfer, genomic rearrangements, and nucleotide polymorphisms. The B. japonicum group presented a larger pangenome and a higher number of nucleotide polymorphisms than the B. diazoefficiens group, possibly due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of the B. japonicum group carry two plasmids. The genetic variability found in both groups is discussed considering the observed differences in their BNF capacity, competitiveness for nodule occupancy, and environmental adaptation.IMPORTANCEToday, Brazil is a global leader in the study and use of biological nitrogen fixation with soybean crops. As Brazilian soils are naturally void of soybean-compatible bradyrhizobia, strain selection programs were established, starting with foreign isolates. Selection searched for adaptation to the local edaphoclimatic conditions, higher efficiency of nitrogen fixation, and strong competitiveness for nodule occupancy. We analyzed the genomes of two parental strains of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens and eight variant strains derived from each parental strain. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation. Our analysis contributes to new insights into the evolution of Bradyrhizobium, and some of the identified differences may be applied as genetic markers to assist strain selection programs.
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Affiliation(s)
- Milena Serenato Klepa
- Soil Biotechnology Laboratory, Embrapa Soja, Londrina, Paraná, Brazil
- CNPq, Brasília, Brazil
| | | | - Mariangela Hungria
- Soil Biotechnology Laboratory, Embrapa Soja, Londrina, Paraná, Brazil
- CNPq, Brasília, Brazil
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7
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Salminen A. Aryl hydrocarbon receptor impairs circadian regulation in Alzheimer's disease: Potential impact on glymphatic system dysfunction. Eur J Neurosci 2024; 60:3901-3920. [PMID: 38924210 DOI: 10.1111/ejn.16450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/23/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
Circadian clocks maintain diurnal rhythms of sleep-wake cycle of 24 h that regulate not only the metabolism of an organism but also many other periodical processes. There is substantial evidence that circadian regulation is impaired in Alzheimer's disease. Circadian clocks regulate many properties known to be disturbed in Alzheimer's patients, such as the integrity of the blood-brain barrier (BBB) as well as the diurnal glymphatic flow that controls waste clearance from the brain. Interestingly, an evolutionarily conserved transcription factor, that is, aryl hydrocarbon receptor (AhR), impairs the function of the core clock proteins and thus could disturb diurnal rhythmicity in the BBB. There is abundant evidence that the activation of AhR signalling inhibits the expression of the major core clock proteins, such as the brain and muscle arnt-like 1 (BMAL1), clock circadian regulator (CLOCK) and period circadian regulator 1 (PER1) in different experimental models. The expression of AhR is robustly increased in the brains of Alzheimer's patients, and protein level is enriched in astrocytes of the BBB. It seems that AhR signalling inhibits glymphatic flow since it is known that (i) activation of AhR impairs the function of the BBB, which is cooperatively interconnected with the glymphatic system in the brain, and (ii) neuroinflammation and dysbiosis of gut microbiota generate potent activators of AhR, which are able to impair glymphatic flow. I will examine current evidence indicating that activation of AhR signalling could disturb circadian functions of the BBB and impair glymphatic flow and thus be involved in the development of Alzheimer's pathology.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
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8
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Dhungel S, Xiao M, Rajesh RP, Kikani C. Nutrient Signaling-Dependent Quaternary Structure Remodeling Drives the Catalytic Activation of metazoan PASK. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.599394. [PMID: 38979257 PMCID: PMC11230368 DOI: 10.1101/2024.06.28.599394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The Per-Arnt-Sim (PAS) domains are characterized by diverse sequences and feature tandemly arranged PAS and PAS-associated C-terminal (PAC) motifs that fold seamlessly to generate the metabolite-sensing PAS domain. Here, using evolutionary scale sequence, domain mapping, and deep learning-based protein structure analysis, we deconstructed the sequence-structure relationship to unearth a novel example of signal-regulated assembly of PAS and PAC subdomains in metazoan PAS domain-regulated kinase (PASK). By comparing protein sequence, domain architecture, and computational protein models between fish, bird, and mammalian PASK orthologs, we propose the existence of previously unrecognized third PAS domain of PASK (PAS-C) formed through long-range intramolecular interactions between the N-terminal PAS fold and the C-terminal PAC fold. We experimentally validated this novel structural design using residue-level cross-linking assays and showed that the PAS-C domain assembly is nutrient-responsive. Furthermore, by combining structural phylogeny approaches with residue-level cross-linking, we revealed that the PAS-C domain assembly links nutrient sensing with quaternary structure reorganization in PASK, stabilizing the kinase catalytic core of PASK. Thus, PAS-C domain assembly likely integrates environmental signals, thereby relaying sensory information for catalytic control of the PASK kinase domain. In conclusion, we theorize that during their horizontal transfer from bacteria to multicellular organisms, PAS domains gained the capacity to integrate environmental signals through dynamic modulation of PAS and PAC motif interaction, adding a new regulatory layer suited for multicellular systems. We propose that metazoan PAS domains are likely to be more dynamic in integrating sensory information than previously considered, and their structural assembly could be targeted by regulatory signals and exploited to develop therapeutic strategies.
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Affiliation(s)
- Sajina Dhungel
- Department of Biology, University of Kentucky, Lexington, Kentucky 40502, USA
| | - Michael Xiao
- Department of Biology, University of Kentucky, Lexington, Kentucky 40502, USA
| | | | - Chintan Kikani
- Department of Biology, University of Kentucky, Lexington, Kentucky 40502, USA
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Graham EB, Garayburu-Caruso VA, Wu R, Zheng J, McClure R, Jones GD. Genomic fingerprints of the world's soil ecosystems. mSystems 2024; 9:e0111223. [PMID: 38722174 PMCID: PMC11237643 DOI: 10.1128/msystems.01112-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/25/2024] [Indexed: 06/19/2024] Open
Abstract
Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes-more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.IMPORTANCEWe address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate.
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Affiliation(s)
- Emily B. Graham
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | | | - Ruonan Wu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jianqiu Zheng
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Ryan McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gerrad D. Jones
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, Oregon, USA
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Quan LF, Chi YY, Dong YZ, Xu S, Chen BX, Li WJ. Identification and characterization of circadian clock genes in the head transcriptome of Conopomorpha sinensis Bradley. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101223. [PMID: 38432103 DOI: 10.1016/j.cbd.2024.101223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/17/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Conopomorpha sinensis Bradley is the most detrimental pest to litchi and longan in China. Adult eclosion, locomotion, mating and oviposition of C. sinensis usually occur at night, regulated by a circadian rhythm. Nevertheless, our understanding of the linkages between adult circadian rhythms and clock genes remains inadequate. To address this gap, transcriptomic analysis was conducted on female and male heads (including antennae) of C. sinensis using the Illumina HiSeq 6000 platform to identify major circadian clock-related genes. The annotated sequences were analyzed by BLASTx, and candidate clock genes were classified based on conservation, predicted domain architectures, and phylogenetic analysis. The analysis revealed a higher conservation of these genes among the compared moths. Further, the expression profile analysis showed a significant spatiotemporal and circadian rhythmic accumulation of some clock genes during development. The candidate clock genes were predominantly expressed in the head, highlighting their crucial function in circadian rhythm regulation. Moreover, CsinPer, CsinTim1, and CsinCry1 displayed similar dynamic expressions with a peak expression level in the 4th age adults, suggesting their involvement in regulation of courtship and mating behaviors. The CsinPer and CsinTim1 mRNA oscillated strongly with a similar phase, containing a peak expression just before the female mating peak. This work will greatly contribute to understanding the circadian clock system of C. sinensis and provide valuable information for further studies of the molecular mechanisms involved in rhythmicity in fruit-boring pests.
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Affiliation(s)
- Lin-Fa Quan
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Yan-Yan Chi
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Yi-Zhi Dong
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Shu Xu
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Bing-Xu Chen
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China.
| | - Wen-Jing Li
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China.
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11
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Nazina TN, Tourova TP, Grouzdev DS, Bidzhieva SK, Poltaraus AB. A Novel View on the Taxonomy of Sulfate-Reducing Bacterium ' Desulfotomaculum salinum' and a Description of a New Species Desulfofundulus salinus sp. nov. Microorganisms 2024; 12:1115. [PMID: 38930497 PMCID: PMC11206085 DOI: 10.3390/microorganisms12061115] [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: 05/08/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Two thermophilic spore-forming sulfate-reducing strains, 435T and 781, were isolated from oil and gas reservoirs in Western Siberia (Russia) about 50 years ago. Both strains were found to be neutrophilic, chemoorganotrophic, anaerobic bacteria, growing at 45-70 °C (optimum, 55-60 °C) and with 0-4.5% (w/v) NaCl (optimum, 0.5-1% NaCl). The major fatty acids were iso-C15:0, iso-C17:0, C16:0, and C18:0. In sulfate-reducing conditions, the strains utilized H2/CO2, formate, lactate, pyruvate, malate, fumarate, succinate, methanol, ethanol, propanol, butanol, butyrate, valerate, and palmitate. In 2005, based on phenotypic characteristics and a 16S rRNA gene sequence analysis, the strains were described as 'Desulfotomaculum salinum' sp. nov. However, this species was not validly published because the type strain was not deposited in two culture collections. In this study, a genomic analysis of strain 435T was carried out to determine its taxonomic affiliation. The genome size of strain 435T was 2.886 Mb with a 55.1% genomic G + C content. The average nucleotide identity and digital DNA-DNA hybridization values were highest between strain 435T and members of the genus Desulfofundulus, 78.7-93.3% and 25.0-52.2%, respectively; these values were below the species delineation cut-offs (<95-96% and <70%). The cumulative phenotypic and phylogenetic data indicate that two strains represent a novel species within the genus Desulfofundulus, for which the name Desulfofundulus salinus sp. nov. is proposed. The type strain is 435T (=VKM B-1492T = DSM 23196T). A genome analysis of strain 435T revealed the genes for dissimilatory sulfate reduction, autotrophic carbon fixation via the Wood-Ljungdahl pathway, hydrogen utilization, methanol and organic acids metabolism, and sporulation, which were confirmed by cultivation studies.
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Affiliation(s)
- Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (T.P.T.); (S.K.B.)
| | - Tatyana P. Tourova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (T.P.T.); (S.K.B.)
| | | | - Salimat K. Bidzhieva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (T.P.T.); (S.K.B.)
| | - Andrey B. Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
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12
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Jones DP. Redox organization of living systems. Free Radic Biol Med 2024; 217:179-189. [PMID: 38490457 PMCID: PMC11313653 DOI: 10.1016/j.freeradbiomed.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
Redox organization governs an underlying simplicity in living systems. Critically, redox reactions enable the essential characteristics of life: extraction of energy from the environment, use of energy to support metabolic and structural organization, use of dynamic redox responses to defend against environmental threats, and use of redox mechanisms to direct differentiation of cells and organ systems essential for reproduction. These processes are sustained through a redox context in which electron donor/acceptor couples are poised at substantially different steady-state redox potentials, some with relatively reducing steady states and others with relatively oxidizing steady states. Redox-sensitive thiols of the redox proteome, as well as low molecular weight redox-active molecules, are maintained individually by the kinetics of oxidation-reduction within this redox system. Recent research has revealed opposing network interactions of the metallome, redox proteome, metabolome and transcriptome, which appear to be an evolved redox response structure to maintain stability of an organism in the presence of variable oxidative environments. Considerable opportunity exists to improve human health through detailed understanding of these redox networks so that targeted interventions can be developed to support new avenues for redox medicine.
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Affiliation(s)
- Dean P Jones
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Whitehead Biomedical Research Building, 615 Michael St, RM205P, Atlanta, GA, 30322, USA.
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13
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Felčíková K, Hovan A, Polák M, Loginov DS, Holotová V, Díaz C, Kožár T, Lee O, Varhač R, Novák P, Bánó G, Sedlák E. Design of AsLOV2 domain as a carrier of light-induced dissociable FMN photosensitizer. Protein Sci 2024; 33:e4921. [PMID: 38501448 PMCID: PMC10949324 DOI: 10.1002/pro.4921] [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: 09/13/2023] [Revised: 01/09/2024] [Accepted: 01/25/2024] [Indexed: 03/20/2024]
Abstract
Flavin mononucleotide (FMN) is a highly efficient photosensitizer (PS) yielding singlet oxygen (1 O2 ). However, its 1 O2 production efficiency significantly decreases upon isoalloxazine ring encapsulation into the protein matrix in genetically encoded photosensitizers (GEPS). Reducing isoalloxazine ring interactions with surrounding amino acids by protein engineering may increase 1 O2 production efficiency GEPS, but at the same time weakened native FMN-protein interactions may cause undesirable FMN dissociation. Here, in contrast, we intentionally induce the FMN release by light-triggered sulfur oxidation of strategically placed cysteines (oxidation-prone amino acids) in the isoalloxazine-binding site due to significantly increased volume of the cysteinyl side residue(s). As a proof of concept, in three variants of the LOV2 domain of Avena sativa (AsLOV2), namely V416C, T418C, and V416C/T418C, the effective 1 O2 production strongly correlated with the efficiency of irradiation-induced FMN dissociation (wild type (WT) < V416C < T418C < V416C/T418C). This alternative approach enables us: (i) to overcome the low 1 O2 production efficiency of flavin-based GEPSs without affecting native isoalloxazine ring-protein interactions and (ii) to utilize AsLOV2, due to its inherent binding propensity to FMN, as a PS vehicle, which is released at a target by light irradiation.
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Affiliation(s)
- Kristína Felčíková
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Andrej Hovan
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Marek Polák
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
- Department of Biochemistry, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Dmitry S. Loginov
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Veronika Holotová
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Carlos Díaz
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Tibor Kožár
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - One‐Sun Lee
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Rastislav Varhač
- Department of Biochemistry, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Petr Novák
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Gregor Bánó
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
- Department of Biochemistry, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
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14
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Lee JH, Oh HM. Effects of Light and Dark Conditions on the Transcriptome of Aging Cultures of Candidatus Puniceispirillum marinum IMCC1322. J Microbiol 2024; 62:297-314. [PMID: 38662311 DOI: 10.1007/s12275-024-00125-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 04/26/2024]
Abstract
To elucidate the function of proteorhodopsin in Candidatus Puniceispirillum marinum strain IMCC1322, a cultivated representative of SAR116, we produced RNA-seq data under laboratory conditions. We examined the transcriptomes of six different cultures, including sets of expression changes under constant dark (DD), constant light (LL), and diel-cycled (LD; 14 h light: 10 h dark) conditions at the exponential and stationary/death phases. Prepared mRNA extracted from the six samples was analyzed on the Solexa Genome Analyzer with 36 cycles. Differentially expressed genes on the IMCC1322 genome were distinguished as four clusters by K-mean clustering and each CDS (n = 2546) was annotated based on the KEGG BRITE hierarchy. Cluster 0 (n = 1573) covered most constitutive genes including proteorhodopsin, retinoids, and glycolysis/TCA cycle. Cluster 1 genes (n = 754) were upregulated in stationary/death phase under constant dark conditions and included genes associated with bacterial defense, membrane transporters, nitrogen metabolism, and senescence signaling. Cluster 2 genes (n = 197) demonstrated upregulation in exponential phase cultures and included genes involved in genes for oxidative phosphorylation, translation factors, and transcription machinery. Cluster 3 (n = 22) contained light-stimulated upregulated genes expressed under stationary/phases. Stringent response genes belonged to cluster 2, but affected genes spanned various cellular processes such as amino acids, nucleotides, translation, transcription, glycolysis, fatty acids, and cell wall components. The coordinated expression of antagonistic stringent genes, including mazG, ppx/gppA, and spoT/relA may provide insight into the controlled cultural response observed between constant light and constant dark conditions in IMCC1322 cultures, regardless of cell numbers and biomass.
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Affiliation(s)
- Ji Hyen Lee
- Department of Pediatrics, Ewha Womans University School of Medicine, Seoul, 07804, Republic of Korea
| | - Hyun-Myung Oh
- Institute of Liberal Arts Education, Pukyong National University, Busan, 48547, Republic of Korea.
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15
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Silva-Parra J, Ramírez-Martínez L, Palafox-Gómez C, Sandu C, López-Bayghen E, Vega L, Elizondo G, Loaeza-Loaeza J, Hernández-Sotelo D, Hernández-Kelly LC, Felder-Schmittbuhl MP, Ortega A. Aryl Hydrocarbon Receptor Involvement in the Sodium-Dependent Glutamate/Aspartate Transporter Regulation in Cerebellar Bergmann Glia Cells. ACS Chem Neurosci 2024; 15:1276-1285. [PMID: 38454572 PMCID: PMC10958506 DOI: 10.1021/acschemneuro.4c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
Glutamate, the major excitatory neurotransmitter in the vertebrate brain, exerts its functions through the activation of specific plasma membrane receptors and transporters. Overstimulation of glutamate receptors results in neuronal cell death through a process known as excitotoxicity. A family of sodium-dependent glutamate plasma membrane transporters is responsible for the removal of glutamate from the synaptic cleft, preventing an excitotoxic insult. Glial glutamate transporters carry out more than 90% of the brain glutamate uptake activity and are responsible for glutamate recycling through the GABA/Glutamate/Glutamine shuttle. The aryl hydrocarbon receptor is a ligand-dependent transcription factor that integrates environmental clues through its ability to heterodimerize with different transcription factors. Taking into consideration the fundamental role of glial glutamate transporters in glutamatergic synapses and that these transporters are regulated at the transcriptional, translational, and localization levels in an activity-dependent fashion, in this contribution, we explored the involvement of the aryl hydrocarbon receptor, as a model of environmental integrator, in the regulation of the glial sodium-dependent glutamate/aspartate transporter. Using the model of chick cerebellar Bergmann glia cells, we report herein that the aryl hydrocarbon receptors exert a time-dependent decrease in the transporter mRNA levels and a diminution of its uptake activity. The nuclear factor kappa light chain enhancer of the activated B cell signaling pathway is involved in this regulation. Our results favor the notion of an environmentally dependent regulation of glutamate removal in glial cells and therefore strengthen the notion of the involvement of glial cells in xenobiotic neurotoxic effects.
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Affiliation(s)
- Janisse Silva-Parra
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Leticia Ramírez-Martínez
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Cecilia Palafox-Gómez
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Cristina Sandu
- Centre
National de la Recherche Scientifique, Université
de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg 00000, France
| | - Esther López-Bayghen
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Libia Vega
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Guillermo Elizondo
- Departamento
de Biología Celular, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Jaqueline Loaeza-Loaeza
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Daniel Hernández-Sotelo
- Facultad
de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39070, Guerrero, Mexico
| | - Luisa C. Hernández-Kelly
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Marie-Paule Felder-Schmittbuhl
- Centre
National de la Recherche Scientifique, Université
de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg 00000, France
| | - Arturo Ortega
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
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16
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Eckle T, Bertazzo J, Khatua TN, Tabatabaei SRF, Bakhtiari NM, Walker LA, Martino TA. Circadian Influences on Myocardial Ischemia-Reperfusion Injury and Heart Failure. Circ Res 2024; 134:675-694. [PMID: 38484024 PMCID: PMC10947118 DOI: 10.1161/circresaha.123.323522] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024]
Abstract
The impact of circadian rhythms on cardiovascular function and disease development is well established, with numerous studies in genetically modified animals emphasizing the circadian molecular clock's significance in the pathogenesis and pathophysiology of myocardial ischemia and heart failure progression. However, translational preclinical studies targeting the heart's circadian biology are just now emerging and are leading to the development of a novel field of medicine termed circadian medicine. In this review, we explore circadian molecular mechanisms and novel therapies, including (1) intense light, (2) small molecules modulating the circadian mechanism, and (3) chronotherapies such as cardiovascular drugs and meal timings. These promise significant clinical translation in circadian medicine for cardiovascular disease. (4) Additionally, we address the differential functioning of the circadian mechanism in males versus females, emphasizing the consideration of biological sex, gender, and aging in circadian therapies for cardiovascular disease.
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Affiliation(s)
- Tobias Eckle
- Department of Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Júlia Bertazzo
- Department of Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Tarak Nath Khatua
- Centre for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Seyed Reza Fatemi Tabatabaei
- Centre for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Naghmeh Moori Bakhtiari
- Centre for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Lori A Walker
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Tami A. Martino
- Centre for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
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17
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Flores-Ibarra A, Maia RNA, Olasz B, Church JR, Gotthard G, Schapiro I, Heberle J, Nogly P. Light-Oxygen-Voltage (LOV)-sensing Domains: Activation Mechanism and Optogenetic Stimulation. J Mol Biol 2024; 436:168356. [PMID: 37944792 DOI: 10.1016/j.jmb.2023.168356] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
The light-oxygen-voltage (LOV) domains of phototropins emerged as essential constituents of light-sensitive proteins, helping initiate blue light-triggered responses. Moreover, these domains have been identified across all kingdoms of life. LOV domains utilize flavin nucleotides as co-factors and undergo structural rearrangements upon exposure to blue light, which activates an effector domain that executes the final output of the photoreaction. LOV domains are versatile photoreceptors that play critical roles in cellular signaling and environmental adaptation; additionally, they can noninvasively sense and control intracellular processes with high spatiotemporal precision, making them ideal candidates for use in optogenetics, where a light signal is linked to a cellular process through a photoreceptor. The ongoing development of LOV-based optogenetic tools, driven by advances in structural biology, spectroscopy, computational methods, and synthetic biology, has the potential to revolutionize the study of biological systems and enable the development of novel therapeutic strategies.
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Affiliation(s)
- Andrea Flores-Ibarra
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Raiza N A Maia
- Department of Chemistry, The University of Texas at Austin, 78712-1224 Austin, TX, USA
| | - Bence Olasz
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | | | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Przemyslaw Nogly
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.
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18
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Leusenko AV, Mironov KS, Los DA. Transmembrane and PAS domains of the histidine kinase Hik33 as regulators of cold and light responses in the cyanobacterium Synechocystis sp. PCC 6803. Biochimie 2024; 218:76-84. [PMID: 37567357 DOI: 10.1016/j.biochi.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/05/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
The PAS (Per-ARNT-Sim) domain is a sensory protein regulatory module found in archaea, prokaryotes, and eukaryotes. Histidine and serine/threonine protein kinases, chemo- and photoreceptors, circadian rhythm regulators, ion channels, phosphodiesterases, and other cellular response regulators are among these proteins. Hik33 is a multifunctional sensory histidine kinase that is implicated in cyanobacterial responses to cold, salt, hyperosmotic, and oxidative stressors. The functional roles of individual Hik33 domains in signal transduction were investigated in this study. Synechocystis Hik33 deletion variants were developed, in which either both or a portion of the transmembrane domains and/or the PAS domain were deleted. Cold stress was applied to the mutant strains either under illumination or in the dark. The findings show that the transmembrane domains govern temperature responses, whereas PAS domain may be involved in regulation of downstream gene expression in light-dependent manner.
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Affiliation(s)
- Anna V Leusenko
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia
| | - Kirill S Mironov
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia
| | - Dmitry A Los
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia.
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19
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Pucelik S, Becker M, Heyber S, Wöhlbrand L, Rabus R, Jahn D, Härtig E. The blue light-dependent LOV-protein LdaP of Dinoroseobacter shibae acts as antirepressor of the PpsR repressor, regulating photosynthetic gene cluster expression. Front Microbiol 2024; 15:1351297. [PMID: 38404597 PMCID: PMC10890935 DOI: 10.3389/fmicb.2024.1351297] [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: 12/06/2023] [Accepted: 01/17/2024] [Indexed: 02/27/2024] Open
Abstract
In the marine α-proteobacterium Dinoroseobacter shibae more than 40 genes of the aerobic anoxygenic photosynthesis are regulated in a light-dependent manner. A genome-wide screen of 5,605 clones from a D. shibae transposon library for loss of pigmentation and changes in bacteriochlorophyll absorbance identified 179 mutant clones. The gene encoding the LOV-domain containing protein Dshi_1135 was identified by its colorless phenotype. The mutant phenotype was complemented by the expression of a Dshi_1135-strep fusion protein in trans. The recombinantly produced and chromatographically purified Dshi_1135 protein was able to undergo a blue light-induced photocycle mediated by bound FMN. Transcriptome analyses revealed an essential role for Dshi_1135 in the light-dependent expression of the photosynthetic gene cluster. Interactomic studies identified the repressor protein PpsR as an interaction partner of Dshi_1135. The physical contact between PpsR and the Dshi_1135 protein was verified in vivo using the bacterial adenylate cyclase-based two-hybrid system. In addition, the antirepressor function of the Dshi_1135 protein was demonstrated in vivo testing of a bchF-lacZ reporter gene fusion in a heterologous Escherichia coli-based host system. We therefore propose to rename the Dshi_1135 protein to LdaP (light-dependent antirepressor of PpsR). Using the bacterial two-hybrid system, it was also shown that cobalamin (B12) is essential for the interaction of the antirepressor PpaA with PpsR. A regulatory model for the photosynthetic gene cluster in D. shibae was derived, including the repressor PpsR, the light-dependent antirepressor LdaP and the B12-dependent antirepressor PpaA.
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Affiliation(s)
- Saskia Pucelik
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Miriam Becker
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Steffi Heyber
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Elisabeth Härtig
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
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20
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Rojas BL, Vazquez-Rivera E, Partch CL, Bradfield CA. Dimerization Rules of Mammalian PAS Proteins. J Mol Biol 2024; 436:168406. [PMID: 38109992 PMCID: PMC10922841 DOI: 10.1016/j.jmb.2023.168406] [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: 08/09/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023]
Abstract
The PAS (PER, ARNT, SIM) protein family plays a vital role in mammalian biology and human disease. This analysis arose from an interest in the signaling mechanics by the Ah receptor (AHR) and the Ah receptor nuclear translocator (ARNT). After more than fifty years by studying this and related mammalian sensor systems, describing the role of PAS domains in signal transduction is still challenging. In this perspective, we attempt to interpret recent studies of mammalian PAS protein structure and consider how this new insight might explain how these domains are employed in human signal transduction with an eye towards developing strategies to target and engineer these molecules for a new generation of therapeutics. Our approach is to integrate our understanding of PAS protein history, cell biology, and molecular biology with recent structural discoveries to help explain the mechanics of mammalian PAS protein signaling. As a learning set, we focus on sequences and crystal structures of mammalian PAS protein dimers that can be visualized using readily available software.
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Affiliation(s)
- Brenda L Rojas
- Molecular and Environmental Toxicology Center, University of Wisconsin at Madison, USA
| | | | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, USA
| | - Christopher A Bradfield
- Molecular and Environmental Toxicology Center, University of Wisconsin at Madison, USA; McArdle Laboratory for Cancer Research. University of Wisconsin, School of Medicine and Public Health, Madison, WI, USA.
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21
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Sharma D, Partch CL. PAS Dimerization at the Nexus of the Mammalian Circadian Clock. J Mol Biol 2024; 436:168341. [PMID: 37924861 DOI: 10.1016/j.jmb.2023.168341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/23/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023]
Abstract
Circadian rhythms are genetically encoded molecular clocks for internal biological timekeeping. Organisms from single-cell bacteria to humans use these clocks to adapt to the external environment and synchronize their physiology and behavior to solar light/dark cycles. Although the proteins that constitute the molecular 'cogs' and give rise to circadian rhythms are now known, we still lack a detailed understanding of how these proteins interact to generate and sustain the ∼24-hour circadian clock. Structural studies have helped to expand the architecture of clock proteins and have revealed the abundance of the only well-defined structured regions in the mammalian clock called Per-ARNT-Sim (PAS) domains. PAS domains are modular, evolutionarily conserved sensory and signaling domains that typically mediate protein-protein interactions. In the mammalian circadian clock, PAS domains modulate homo and heterodimerization of several core clock proteins that assemble into transcription factors or repressors. This review will focus on the functional importance of the PAS domains in the circadian clock from a biophysical and biochemical standpoint and describe their roles in clock protein interactions and circadian timekeeping.
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Affiliation(s)
- Diksha Sharma
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA, United States
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA, United States; Center for Circadian Biology, University of California San Diego, CA, United States.
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22
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Caramello N, Royant A. From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons. Acta Crystallogr D Struct Biol 2024; 80:60-79. [PMID: 38265875 PMCID: PMC10836399 DOI: 10.1107/s2059798323011002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024] Open
Abstract
Over the last decade, the development of time-resolved serial crystallography (TR-SX) at X-ray free-electron lasers (XFELs) and synchrotrons has allowed researchers to study phenomena occurring in proteins on the femtosecond-to-minute timescale, taking advantage of many technical and methodological breakthroughs. Protein crystals of various sizes are presented to the X-ray beam in either a static or a moving medium. Photoactive proteins were naturally the initial systems to be studied in TR-SX experiments using pump-probe schemes, where the pump is a pulse of visible light. Other reaction initiations through small-molecule diffusion are gaining momentum. Here, selected examples of XFEL and synchrotron time-resolved crystallography studies will be used to highlight the specificities of the various instruments and methods with respect to time resolution, and are compared with cryo-trapping studies.
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Affiliation(s)
- Nicolas Caramello
- Structural Biology Group, European Synchrotron Radiation Facility, 1 Avenue des Martyrs, CS 40220, 38043 Grenoble CEDEX 9, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 1 Avenue des Martyrs, CS 40220, 38043 Grenoble CEDEX 9, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, CS 10090, 38044 Grenoble CEDEX 9, France
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23
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Xiao M, Dhungel S, Azad R, Favaro DC, Rajesh RP, Gardner KH, Kikani CK. Signal-regulated Unmasking of Nuclear Localization Motif in the PAS Domain Regulates the Nuclear Translocation of PASK. J Mol Biol 2024; 436:168433. [PMID: 38182104 PMCID: PMC10922792 DOI: 10.1016/j.jmb.2023.168433] [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: 09/11/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024]
Abstract
The ligand-regulated PAS domains are one of the most diverse signal-integrating domains found in proteins from prokaryotes to humans. By biochemically connecting cellular processes with their environment, PAS domains facilitate an appropriate cellular response. PAS domain-containing Kinase (PASK) is an evolutionarily conserved protein kinase that plays important signaling roles in mammalian stem cells to establish stem cell fate. We have shown that the nuclear translocation of PASK is stimulated by differentiation signaling cues in muscle stem cells. However, the mechanistic basis of the regulation of PASK nucleo-cytoplasmic translocation remains unknown. Here, we show that the PAS-A domain of PASK contains a putative monopartite nuclear localization sequence (NLS) motif. This NLS is inhibited in cells through intramolecular association with a short linear motif, termed the PAS Interacting Motif (PIM), found upstream of the kinase domain. This interaction serves to retain PASK in the cytosol in the absence of signaling cues. Consistent with that, we show that metabolic inputs induce PASK nuclear import, likely by disrupting this association. We suggest that a route for such linkage may occur through the PAS-A ligand binding cavity. We show that PIM recruitment and artificial ligand binding to the PAS-A domain occur at neighboring locations that could facilitate metabolic control of the PAS-PIM interaction. Thus, the intramolecular interaction in PASK integrates metabolic signaling cues for nuclear translocation and could be targeted to control the balance between self-renewal and differentiation in stem cells.
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Affiliation(s)
- Michael Xiao
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
| | - Sajina Dhungel
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
| | - Roksana Azad
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA; Ph.D. Program in Biochemistry, Graduate Center, City University of New York, NY 10016, USA
| | - Denize C Favaro
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
| | | | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA; Department of Chemistry and Biochemistry, City College of New York, NY 10031, USA; Ph.D. Programs in Biochemistry, Chemistry and Biology Ph.D. Programs, Graduate Center, City University of New York, NY 10016, USA.
| | - Chintan K Kikani
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA.
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24
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Nie H, Nie L, Xiao Y, Song M, Zhou T, He J, Chen W, Huang Q. The phosphodiesterase DibA interacts with the c-di-GMP receptor LapD and specifically regulates biofilm in Pseudomonas putida. Mol Microbiol 2024; 121:1-17. [PMID: 37927230 DOI: 10.1111/mmi.15189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/30/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023]
Abstract
The ubiquitous bacterial second messenger c-di-GMP is synthesized by diguanylate cyclase and degraded by c-di-GMP-specific phosphodiesterase. The genome of Pseudomonas putida contains dozens of genes encoding diguanylate cyclase/phosphodiesterase, but the phenotypical-genotypical correlation and functional mechanism of these genes are largely unknown. Herein, we characterize the function and mechanism of a P. putida phosphodiesterase named DibA. DibA consists of a PAS domain, a GGDEF domain, and an EAL domain. The EAL domain is active and confers DibA phosphodiesterase activity. The GGDEF domain is inactive, but it promotes the phosphodiesterase activity of the EAL domain via binding GTP. Regarding phenotypic regulation, DibA modulates the cell surface adhesin LapA level in a c-di-GMP receptor LapD-dependent manner, thereby inhibiting biofilm formation. Moreover, DibA interacts and colocalizes with LapD in the cell membrane, and the interaction between DibA and LapD promotes the PDE activity of DibA. Besides, except for interacting with DibA and LapD itself, LapD is found to interact with 11 different potential diguanylate cyclases/phosphodiesterases in P. putida, including the conserved phosphodiesterase BifA. Overall, our findings demonstrate the functional mechanism by which DibA regulates biofilm formation and expand the understanding of the LapD-mediated c-di-GMP signaling network in P. putida.
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Affiliation(s)
- Hailing Nie
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Liang Nie
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Yujie Xiao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Miaomiao Song
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Tiantian Zhou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Jinzhi He
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wenli Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
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25
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Chowdhury G, Biswas S, Dholey Y, Panja P, Das S, Adak S. Importance of aspartate 4 in the Mg 2+ dependent regulation of Leishmania major PAS domain-containing phosphoglycerate kinase. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140964. [PMID: 37726028 DOI: 10.1016/j.bbapap.2023.140964] [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: 07/05/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/21/2023]
Abstract
Magnesium is an important divalent cation for the regulation of catalytic activity. Recently, we have described that the Mg2+ binding through the PAS domain inhibits the phosphoglycerate kinase (PGK) activity in PAS domain-containing PGK from Leishmania major (LmPAS-PGK) at neutral pH 7.5, but PGK activity is derepressed at acidic pH 5.5. The acidic residue within the PAS domain of LmPAS-PGK is expected to bind the cofactor Mg2+ ion at neutral pH, but which specific acidic residue(s) is/are responsible for the Mg2+ binding is still unknown. To identify the residues, we exploited mutational studies of all acidic (twelve Asp/Glu) residues in the PAS domain for plausible Mg2+ binding. Mg2+ ion-dependent repression at pH 7.5 is withdrawn by substitution of Asp-4 with Ala, whereas other acidic residue mutants (D16A, D22A, D24A, D29A, D43A, D44A, D60A, D63A, D77A, D87A, and E107A) showed similar features compared to the wild-type protein. Fluorescence spectroscopic studies and isothermal titration calorimetry analysis showed that the Asp-4 is crucial for Mg2+ binding in the absence of both PGK's substrates. These results suggest that Asp-4 residue in the regulatory (PAS) domain of wild type enzymes is required for Mg2+ dependent repressed state of the catalytic PGK domain at neutral pH.
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Affiliation(s)
- Gaurab Chowdhury
- Division of Structural Biology & Bio-informatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Saroj Biswas
- Division of Structural Biology & Bio-informatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Yuthika Dholey
- Division of Structural Biology & Bio-informatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Puja Panja
- Division of Structural Biology & Bio-informatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Sumit Das
- Division of Structural Biology & Bio-informatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Subrata Adak
- Division of Structural Biology & Bio-informatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India.
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26
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Zhang R, Wang Y. EvgS/EvgA, the unorthodox two-component system regulating bacterial multiple resistance. Appl Environ Microbiol 2023; 89:e0157723. [PMID: 38019025 PMCID: PMC10734491 DOI: 10.1128/aem.01577-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE EvgS/EvgA, one of the five unorthodox two-component systems in Escherichia coli, plays an essential role in adjusting bacterial behaviors to adapt to the changing environment. Multiple resistance regulated by EvgS/EvgA endows bacteria to survive in adverse conditions such as acidic pH, multidrug, and heat. In this minireview, we summarize the specific structures and regulation mechanisms of EvgS/EvgA and its multiple resistance. By discussing several unresolved issues and proposing our speculations, this review will be helpful and enlightening for future directions about EvgS/EvgA.
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Affiliation(s)
- Ruizhen Zhang
- MoE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yan Wang
- MoE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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27
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Arkhipov DV, Lomin SN, Romanov GA. A Model of the Full-Length Cytokinin Receptor: New Insights and Prospects. Int J Mol Sci 2023; 25:73. [PMID: 38203244 PMCID: PMC10779265 DOI: 10.3390/ijms25010073] [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: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Cytokinins (CK) are one of the most important classes of phytohormones that regulate a wide range of processes in plants. A CK receptor, a sensor hybrid histidine kinase, was discovered more than 20 years ago, but the structural basis for its signaling is still a challenge for plant biologists. To date, only two fragments of the CK receptor structure, the sensory module and the receiver domain, were experimentally resolved. Some other regions were built up by molecular modeling based on structures of proteins homologous to CK receptors. However, in the long term, these data have proven insufficient for solving the structure of the full-sized CK receptor. The functional unit of CK receptor is the receptor dimer. In this article, a molecular structure of the dimeric form of the full-length CK receptor based on AlphaFold Multimer and ColabFold modeling is presented for the first time. Structural changes of the receptor upon interacting with phosphotransfer protein are visualized. According to mathematical simulation and available data, both types of dimeric receptor complexes with hormones, either half- or fully liganded, appear to be active in triggering signals. In addition, the prospects of using this and similar models to address remaining fundamental problems of CK signaling were outlined.
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Affiliation(s)
| | | | - Georgy A. Romanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia; (D.V.A.); (S.N.L.)
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28
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Zhou B, Garber JM, Vlach J, Azadi P, Ng KKS, Escalante-Semerena JC, Szymanski CM. Campylobacter jejuni uses energy taxis and a dehydrogenase enzyme for l-fucose chemotaxis. mBio 2023; 14:e0273223. [PMID: 38032212 PMCID: PMC10746189 DOI: 10.1128/mbio.02732-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE In this study, we identify a separate role for the Campylobacter jejuni l-fucose dehydrogenase in l-fucose chemotaxis and demonstrate that this mechanism is not only limited to C. jejuni but is also present in Burkholderia multivorans. We now hypothesize that l-fucose energy taxis may contribute to the reduction of l-fucose-metabolizing strains of C. jejuni from the gastrointestinal tract of breastfed infants, selecting for isolates with increased colonization potential.
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Affiliation(s)
- Bibi Zhou
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Jolene M. Garber
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Jiri Vlach
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Kenneth K. S. Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | | | - Christine M. Szymanski
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
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29
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Arshi SA, Chauhan M, Sharma A. Disruption of the FMN-A524 interaction cascade and Glu513-induced collapse of the hydrophobic barrier promotes light-induced Jα-helix unfolding in AsLOV2. Biophys J 2023; 122:4670-4685. [PMID: 37978801 PMCID: PMC10754690 DOI: 10.1016/j.bpj.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/10/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
The C-terminal Jα-helix of the Avena sativa's Light Oxygen and Voltage (AsLOV2) protein, unfolds on exposure to blue light. This characteristic seeks relevance in applications related to engineering novel biological photoswitches. Using molecular dynamics simulations and the Markov state modeling (MSM) approach we provide the mechanism that explains the stepwise unfolding of the Jα-helix. The unfolding was resolved into seven steps represented by the structurally distinguishable states distributed over the initiation and the post initiation phases. Whereas, the initiation phase occurs due to the collapse of the interaction cascade FMN-Q513-N492-L480-W491-Q479-V520-A524, the onset of the post initiation phase is marked by breaking of the hydrophobic interactions between the Jα-helix and the Iβ-strand. This study indicates that the displacement of N492 out of the FMN binding pocket, not necessarily requiring Q513, is essential for the initiation of the Jα-helix unfolding. Rather, the structural reorientation of Q513 activates the protein to cross the hydrophobic barrier and enter the post initiation phase. Similarly, the structural deviations in N482, rather than its integral role in unfolding, could enhance the unfolding rates. Furthermore, the MSM studies on the wild-type and the Q513 mutant, provide the spatiotemporal roadmap that lay out the possible pathways of structural transition between the dark and the light states of the protein. Overall, the study provides insights useful to enhance the performance of AsLOV2-based photoswitches.
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Affiliation(s)
- Syeda Amna Arshi
- Multidisciplinary Centre for Advance Research and Studies, Jamia Millia Islamia, New Delhi, India
| | - Manisha Chauhan
- Multidisciplinary Centre for Advance Research and Studies, Jamia Millia Islamia, New Delhi, India
| | - Amit Sharma
- Multidisciplinary Centre for Advance Research and Studies, Jamia Millia Islamia, New Delhi, India.
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30
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Zhang R, Yu C, Zeh HJ, Wang H, Kroemer G, Klionsky DJ, Billiar TR, Kang R, Tang D. Nuclear localization of STING1 competes with canonical signaling to activate AHR for commensal and intestinal homeostasis. Immunity 2023; 56:2736-2754.e8. [PMID: 38016467 PMCID: PMC10842782 DOI: 10.1016/j.immuni.2023.11.001] [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: 01/24/2023] [Revised: 09/22/2023] [Accepted: 11/01/2023] [Indexed: 11/30/2023]
Abstract
Extensive studies demonstrate the importance of the STING1 (also known as STING) protein as a signaling hub that coordinates immune and autophagic responses to ectopic DNA in the cytoplasm. Here, we report a nuclear function of STING1 in driving the activation of the transcription factor aryl hydrocarbon receptor (AHR) to control gut microbiota composition and homeostasis. This function was independent of DNA sensing and autophagy and showed competitive inhibition with cytoplasmic cyclic guanosine monophosphate (GMP)-AMP synthase (CGAS)-STING1 signaling. Structurally, the cyclic dinucleotide binding domain of STING1 interacted with the AHR N-terminal domain. Proteomic analyses revealed that STING1-mediated transcriptional activation of AHR required additional nuclear partners, including positive and negative regulatory proteins. Although AHR ligands could rescue colitis pathology and dysbiosis in wild-type mice, this protection was abrogated by mutational inactivation of STING1. These findings establish a key framework for understanding the nuclear molecular crosstalk between the microbiota and the immune system.
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Affiliation(s)
- Ruoxi Zhang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chunhua Yu
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Herbert J Zeh
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Haichao Wang
- Laboratory of Emergency Medicine, North Shore University Hospital and the Feinsteins Institute for Medical Research, Manhasset, NY 11030, USA
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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31
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Gupta A, Pandey P, Gupta R, Tiwari S, Singh SP. Responding to light signals: a comprehensive update on photomorphogenesis in cyanobacteria. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1915-1930. [PMID: 38222287 PMCID: PMC10784256 DOI: 10.1007/s12298-023-01386-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 01/16/2024]
Abstract
Cyanobacteria are ancestors of chloroplast and perform oxygen-evolving photosynthesis similar to higher plants and algae. However, an obligatory requirement of photons for their growth results in the exposure of cyanobacteria to varying light conditions. Therefore, the light environment could act as a signal to drive the developmental processes, in addition to photosynthesis, in cyanobacteria. These Gram-negative prokaryotes exhibit characteristic light-dependent developmental processes that maximize their fitness and resource utilization. The development occurring in response to radiance (photomorphogenesis) involves fine-tuning cellular physiology, morphology and metabolism. The best-studied example of cyanobacterial photomorphogenesis is chromatic acclimation (CA), which allows a selected number of cyanobacteria to tailor their light-harvesting antenna called phycobilisome (PBS). The tailoring of PBS under existing wavelengths and abundance of light gives an advantage to cyanobacteria over another photoautotroph. In this work, we will provide a comprehensive update on light-sensing, molecular signaling and signal cascades found in cyanobacteria. We also include recent developments made in other aspects of CA, such as mechanistic insights into changes in the size and shape of cells, filaments and carboxysomes.
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Affiliation(s)
- Anjali Gupta
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Priyul Pandey
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Rinkesh Gupta
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Sapna Tiwari
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Shailendra Pratap Singh
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
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32
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Xiao M, Dhungel S, Azad R, Favaro DC, Rajesh RP, Gardner KH, Kikani CK. Signal-regulated unmasking of the nuclear localization motif in the PAS domain regulates the nuclear translocation of PASK. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556462. [PMID: 37732199 PMCID: PMC10508781 DOI: 10.1101/2023.09.06.556462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The ligand-regulated PAS domains are one of the most diverse signal-integrating domains found in proteins from prokaryotes to humans. By biochemically connecting cellular processes with their environment, PAS domains facilitate an appropriate cellular response. PAS domain-containing Kinase (PASK) is an evolutionarily conserved protein kinase that plays important signaling roles in mammalian stem cells to establish stem cell fate. We have shown that the nuclear translocation of PASK is stimulated by differentiation signaling cues in muscle stem cells. However, the mechanistic basis of the regulation of PASK nucleo-cytoplasmic translocation remains unknown. Here, we show that the PAS-A domain of PASK contains a putative monopartite nuclear localization sequence (NLS) motif. This NLS is inhibited in cells via intramolecular association with a short linear motif, termed the PAS Interacting Motif (PIM), found upstream of the kinase domain. The interaction between the PAS-A domain and PIM is evolutionarily conserved and serves to retain PASK in the cytosol in the absence of signaling cues. Consistent with that, we show that metabolic inputs induce PASK nuclear import, likely by disrupting the PAS-A: PIM association. We suggest that a route for such linkage may occur through the PAS-A ligand binding cavity. We show that PIM recruitment and artificial ligand binding to the PAS-A domain occur at neighboring locations that could facilitate metabolic control of the PAS-PIM interaction. Thus, the PAS-A domain of PASK integrates metabolic signaling cues for nuclear translocation and could be targeted to control the balance between self-renewal and differentiation in stem cells.
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Affiliation(s)
- Michael Xiao
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
| | - Sajina Dhungel
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
| | - Roksana Azad
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
- Ph.D. Program in Biochemistry, Graduate Center, City University of New York, NY 10016, USA
| | - Denize C. Favaro
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
| | | | - Kevin H. Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
- Department of Chemistry and Biochemistry, City College of New York, NY 10031, USA
- Ph.D. Programs in Biochemistry, Chemistry and Biology Ph.D. Programs, Graduate Center, City University of New York, NY 10016, USA
| | - Chintan K. Kikani
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
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Boubsi F, Hoff G, Arguelles Arias A, Steels S, Andrić S, Anckaert A, Roulard R, Rigolet A, van Wuytswinkel O, Ongena M. Pectic homogalacturonan sensed by Bacillus acts as host associated cue to promote establishment and persistence in the rhizosphere. iScience 2023; 26:107925. [PMID: 37790276 PMCID: PMC10543691 DOI: 10.1016/j.isci.2023.107925] [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: 04/07/2023] [Revised: 07/19/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
Bacillus velezensis isolates are among the most promising plant-associated beneficial bacteria used as biocontrol agents. However, various aspects of the chemical communication between the plant and these beneficials, determining root colonization ability, remain poorly described. Here we investigated the molecular basis of such interkingdom interaction occurring upon contact between Bacillus velezensis and its host via the sensing of pectin backbone homogalacturonan (HG). We showed that B. velezensis stimulates key developmental traits via a dynamic process involving two conserved pectinolytic enzymes. This response integrates transcriptional changes leading to the switch from planktonic to sessile cells, a strong increase in biofilm formation, and an accelerated sporulation dynamics while conserving the potential to efficiently produce specialized secondary metabolites. As a whole, we anticipate that this response of Bacillus to cell wall-derived host cues contributes to its establishment and persistence in the competitive rhizosphere niche and ipso facto to its activity as biocontrol agent.
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Affiliation(s)
- Farah Boubsi
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Grégory Hoff
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Anthony Arguelles Arias
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Sébastien Steels
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Sofija Andrić
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Adrien Anckaert
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Romain Roulard
- UMRT INRAe 1158 Plant Biology and Innovation, University of Picardie Jules Verne, UFR des Sciences, 80039 Amiens, France
| | - Augustin Rigolet
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Olivier van Wuytswinkel
- UMRT INRAe 1158 Plant Biology and Innovation, University of Picardie Jules Verne, UFR des Sciences, 80039 Amiens, France
| | - Marc Ongena
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
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Hwang Y, Na JG, Lee SJ. Transcriptional regulation of soluble methane monooxygenase via enhancer-binding protein derived from Methylosinus sporium 5. Appl Environ Microbiol 2023; 89:e0210422. [PMID: 37668365 PMCID: PMC10537576 DOI: 10.1128/aem.02104-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/07/2023] [Indexed: 09/06/2023] Open
Abstract
Methane is a major greenhouse gas, and methanotrophs regulate the methane level in the carbon cycle. Soluble methane monooxygenase (sMMO) is expressed in various methanotroph genera, including Alphaproteobacteria and Gammaproteobacteria, and catalyzes the hydroxylation of methane to methanol. It has been proposed that MmoR regulates the expression of sMMO as an enhancer-binding protein under copper-limited conditions; however, details on this transcriptional regulation remain limited. Herein, we elucidate the transcriptional pathway of sMMO depending on copper ion concentration, which affects the interaction of MmoR and sigma factor. MmoR and sigma-54 (σ54) from Methylosinus sporium 5 were successfully overexpressed in Escherichia coli and purified to investigate sMMO transcription in methanotrophs. The results indicated that σ54 binds to a promoter positioned -24 (GG) and -12 (TGC) upstream between mmoG and mmoX1. The binding affinity and selectivity are lower (Kd = 184.6 ± 6.2 nM) than those of MmoR. MmoR interacts with the upstream activator sequence (UAS) with a strong binding affinity (Kd = 12.5 ± 0.5 nM). Mutational studies demonstrated that MmoR has high selectivity to its binding partner (ACA-xx-TGT). Titration assays have demonstrated that MmoR does not coordinate with copper ions directly; however, its binding affinity to UAS decreases in a low-copper-containing medium. MmoR strongly interacts with adenosine triphosphate (Kd = 62.8 ± 0.5 nM) to generate RNA polymerase complex. This study demonstrated that the binding events of both MmoR and σ54 that regulate transcription in M. sporium 5 depend on the copper ion concentration. IMPORTANCE This study provides biochemical evidence of transcriptional regulation of soluble methane monooxygenase (sMMO) in methanotrophs that control methane levels in ecological systems. Previous studies have proposed transcriptional regulation of MMOs, including sMMO and pMMO, while we provide further evidence to elucidate its mechanism using a purified enhancer-binding protein (MmoR) and transcription factor (σ54). The characterization studies of σ54 and MmoR identified the promoter binding sites and enhancer-binding sequences essential for sMMO expression. Our findings also demonstrate that MmoR functions as a trigger for sMMO expression due to the high specificity and selectivity for enhancer-binding sequences. The UV-visible spectrum of purified MmoR suggested an iron coordination like other GAF domain, and that ATP is essential for the initiation of enhancer elements. Binding assays indicated that these interactions are blocked by the copper ion. These results provide novel insights into gene regulation of methanotrophs.
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Affiliation(s)
- Yunha Hwang
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
| | - Jeong-Geol Na
- Department of Chemical Engineering, Sogang University , Seoul, South Korea
| | - Seung Jae Lee
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
- Institute of Molecular Biology and Genetics, Jeonbuk National University , Jeonju, South Korea
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35
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Laothamatas I, Rasmussen ES, Green CB, Takahashi JS. Metabolic and chemical architecture of the mammalian circadian clock. Cell Chem Biol 2023; 30:1033-1052. [PMID: 37708890 PMCID: PMC10631358 DOI: 10.1016/j.chembiol.2023.08.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/20/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
Circadian rhythms are endogenous periodic biological processes that occur on a daily timescale. These rhythms are generated by a transcriptional/translational feedback loop that consists of the CLOCK-BMAL1 heterodimeric transcriptional activator complex and the PER1/2-CRY1/2-CK1δ/ε repressive complex. The output pathways of this molecular feedback loop generate circadian rhythmicity in various biological processes. Among these, metabolism is a primary regulatory target of the circadian clock which can also feedback to modulate clock function. This intertwined relationship between circadian rhythms and metabolism makes circadian clock components promising therapeutic targets. Despite this, pharmacological therapeutics that target the circadian clock are relatively rare. In this review, we hope to stimulate interest in chemical chronobiology by providing a comprehensive background on the molecular mechanism of mammalian circadian rhythms and their connection to metabolism, highlighting important studies in the chemical approach to circadian research, and offering our perspectives on future developments in the field.
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Affiliation(s)
- Isara Laothamatas
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Emil Sjulstok Rasmussen
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Carla B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Xing J, Gumerov VM, Zhulin IB. Origin and functional diversification of PAS domain, a ubiquitous intracellular sensor. SCIENCE ADVANCES 2023; 9:eadi4517. [PMID: 37647406 PMCID: PMC10468136 DOI: 10.1126/sciadv.adi4517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Signal perception is a key function in regulating biological activities and adapting to changing environments. Per-Arnt-Sim (PAS) domains are ubiquitous sensors found in diverse receptors in bacteria, archaea, and eukaryotes, but their origins, distribution across the tree of life, and extent of their functional diversity are not fully characterized. Here, we show that using sequence conservation and structural information, it is possible to propose specific and potential functions for a large portion of nearly 3 million PAS domains. Our analysis suggests that PAS domains originated in bacteria and were horizontally transferred to archaea and eukaryotes. We reveal that gas sensing via a heme cofactor evolved independently in several lineages, whereas redox and light sensing via flavin adenine dinucleotide and flavin mononucleotide cofactors have the same origin. The close relatedness of human PAS domains to those in bacteria provides an opportunity for drug design by exploring potential natural ligands and cofactors for bacterial homologs.
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Affiliation(s)
- Jiawei Xing
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH USA
| | - Vadim M. Gumerov
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH USA
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH USA
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Cochard C, Caby M, Gruau P, Madec E, Marceau M, Macavei I, Lemoine J, Le Danvic C, Bouchart F, Delrue B, Bontemps-Gallo S, Lacroix JM. Emergence of the Dickeya genus involved duplication of the OmpF porin and the adaptation of the EnvZ-OmpR signaling network. Microbiol Spectr 2023; 11:e0083323. [PMID: 37642428 PMCID: PMC10581057 DOI: 10.1128/spectrum.00833-23] [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: 02/24/2023] [Accepted: 07/06/2023] [Indexed: 08/31/2023] Open
Abstract
Genome evolution, and more specifically gene duplication, is a key process shaping host-microorganism interaction. The conserved paralogs usually provide an advantage to the bacterium to thrive. If not, these genes become pseudogenes and disappear. Here, we show that during the emergence of the genus Dickeya, the gene encoding the porin OmpF was duplicated. Our results show that the ompF2 expression is deleterious to the virulence of Dickeya dadantii, the agent causing soft rot disease. Interestingly, ompF2 is regulated while ompF is constitutive but activated by the EnvZ-OmpR two-component system. In vitro, acidic pH triggers the system. The pH measured in four eudicotyledons increased from an initial pH of 5.5 to 7 within 8 h post-infection. Then, the pH decreased to 5.5 at 10 h post-infection and until full maceration of the plant tissue. Yet, the production of phenolic acids by the plant's defenses prevents the activation of the EnvZ-OmpR system to avoid the ompF2 expression even though environmental conditions should trigger this system. We highlight that gene duplication in a pathogen is not automatically an advantage for the infectious process and that, there was a need for our model organism to adapt its genetic regulatory networks to conserve these duplicated genes. IMPORTANCE Dickeya species cause various diseases in a wide range of crops and ornamental plants. Understanding the molecular program that allows the bacterium to colonize the plant is key to developing new pest control methods. Unlike other enterobacterial pathogens, Dickeya dadantii, the causal agent of soft rot disease, does not require the EnvZ-OmpR system for virulence. Here, we showed that during the emergence of the genus Dickeya, the gene encoding the porin OmpF was duplicated and that the expression of ompF2 was deleterious for virulence. We revealed that while the EnvZ-OmpR system was activated in vitro by acidic pH and even though the pH was acidic when the plant is colonized, this system was repressed by phenolic acid (generated by the plant's defenses). These results provide a unique- biologically relevant-perspective on the consequence of gene duplication and the adaptive nature of regulatory networks to retain the duplicated gene.
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Affiliation(s)
- Clémence Cochard
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Marine Caby
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Peggy Gruau
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Edwige Madec
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Michael Marceau
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Iulia Macavei
- Univ. Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, Villeurbanne, France
| | - Jérôme Lemoine
- Univ. Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, Villeurbanne, France
| | - Chrystelle Le Danvic
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- R&D Department, ALLICE, Paris, France
| | - Franck Bouchart
- Université Polytechnique Hauts-de-France, EA 2443 - LMCPA - Laboratoire des Matériaux Céramiques et Procédés Associés, Valenciennes, France
| | - Brigitte Delrue
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Sébastien Bontemps-Gallo
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Jean-Marie Lacroix
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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Yin Z, Shen D, Zhao Y, Peng H, Liu J, Dou D. Cross-kingdom analyses of transmembrane protein kinases show their functional diversity and distinct origins in protists. Comput Struct Biotechnol J 2023; 21:4070-4078. [PMID: 37649710 PMCID: PMC10463195 DOI: 10.1016/j.csbj.2023.08.007] [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: 03/20/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023] Open
Abstract
Transmembrane kinases (TMKs) are important mediators of cellular signaling cascades. The kinase domains of most metazoan and plant TMKs belong to the serine/threonine/tyrosine kinase (S/T/Y-kinase) superfamily. They share a common origin with prokaryotic kinases and have diversified into distinct subfamilies. Diverse members of the eukaryotic crown radiation such as amoebae, ciliates, and red and brown algae (grouped here under the umbrella term "protists") have long diverged from higher eukaryotes since their ancient common ancestry, making them ideal organisms for studying TMK evolution. Here, we developed an accurate and high-throughput pipeline to predict TMKomes in cellular organisms. Cross-kingdom analyses revealed distinct features of TMKomes in each grouping. Two-transmembrane histidine kinases constitute the main TMKomes of bacteria, while metazoans, plants, and most protists have a large proportion of single-pass TM S/T/Y-kinases. Phylogenetic analyses classified most protist S/T/Y-kinases into three clades, with clades II and III specifically expanded in amoebae and oomycetes, respectively. In contrast, clade I kinases were widespread in all protists examined here, and likely shared a common origin with other eukaryotic S/T/Y-kinases. Functional annotation further showed that most non-kinase domains were grouping-specific, suggesting that their recombination with the more conserved kinase domains led to the divergence of S/T/Y-kinases. However, we also found that protist leucine-rich repeat (LRR)- and G-protein-coupled receptor (GPCR)-type TMKs shared similar sensory domain architectures with respective plant and animal TMKs, despite that they belong to distinct kinase subfamilies. Collectively, our study revealed the functional diversity of TMKomes and the distinct origins of S/T/Y-kinases in protists.
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Affiliation(s)
- Zhiyuan Yin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yaning Zhao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Peng
- USDA Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, USA
| | - Jinding Liu
- Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
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Daffern N, Kelley K, Villegas JA, Radhakrishnan I. Prostaglandins as Candidate Ligands for a Per-ARNT-Sim (PAS) Domain of Steroid Receptor Coactivator 1 (SRC1). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548854. [PMID: 37502902 PMCID: PMC10369948 DOI: 10.1101/2023.07.13.548854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Steroid receptor coactivators (SRCs) comprise a family of three paralogous proteins commonly recruited by eukaryotic transcription factors. Each SRC harbors two tandem Per-ARNT-Sim (PAS) domains that are broadly distributed that bind small molecules and regulate interactions. Using computational docking, solution NMR, mass spectrometry, and molecular dynamics simulations, we show that the SRC1 PAS-B domain can bind to certain prostaglandins (PGs) either non-covalently to a surface that overlaps with the site used to engage transcription factors or covalently to a single, specific, conserved cysteine residue next to a solvent accessible hydrophobic pocket. This pocket is in proximity to the canonical transcription factor binding site, but on the opposite side of the domain, suggesting a potential mode of regulating transcriptional activator-coactivator interactions.
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Affiliation(s)
- Nicolas Daffern
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Kade Kelley
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - José A Villegas
- Department of Pharmaceutical Sciences, University of Illinois Chicago, Chicago, IL 60612
| | - Ishwar Radhakrishnan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
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40
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Yu Z, Zhang W, Yang H, Chou SH, Galperin MY, He J. Gas and light: triggers of c-di-GMP-mediated regulation. FEMS Microbiol Rev 2023; 47:fuad034. [PMID: 37339911 PMCID: PMC10505747 DOI: 10.1093/femsre/fuad034] [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: 02/01/2023] [Revised: 06/01/2023] [Accepted: 06/17/2023] [Indexed: 06/22/2023] Open
Abstract
The widespread bacterial second messenger c-di-GMP is responsible for regulating many important physiological functions such as biofilm formation, motility, cell differentiation, and virulence. The synthesis and degradation of c-di-GMP in bacterial cells depend, respectively, on diguanylate cyclases and c-di-GMP-specific phosphodiesterases. Since c-di-GMP metabolic enzymes (CMEs) are often fused to sensory domains, their activities are likely controlled by environmental signals, thereby altering cellular c-di-GMP levels and regulating bacterial adaptive behaviors. Previous studies on c-di-GMP-mediated regulation mainly focused on downstream signaling pathways, including the identification of CMEs, cellular c-di-GMP receptors, and c-di-GMP-regulated processes. The mechanisms of CME regulation by upstream signaling modules received less attention, resulting in a limited understanding of the c-di-GMP regulatory networks. We review here the diversity of sensory domains related to bacterial CME regulation. We specifically discuss those domains that are capable of sensing gaseous or light signals and the mechanisms they use for regulating cellular c-di-GMP levels. It is hoped that this review would help refine the complete c-di-GMP regulatory networks and improve our understanding of bacterial behaviors in changing environments. In practical terms, this may eventually provide a way to control c-di-GMP-mediated bacterial biofilm formation and pathogenesis in general.
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Affiliation(s)
- Zhaoqing Yu
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, Jiangsu 210014, PR China
| | - Wei Zhang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - He Yang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Shan-Ho Chou
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jin He
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
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Silva AM, Pedrini N, Pupin B, Roberts DW, Rangel DEN. Asphyxiation of Metarhizium robertsii during mycelial growth produces conidia with increased stress tolerance via increased expression of stress-related genes. Fungal Biol 2023; 127:1209-1217. [PMID: 37495310 DOI: 10.1016/j.funbio.2023.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/07/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023]
Abstract
Little is known about the impact of hypoxia and anoxia during mycelial growth on tolerance to different stress conditions of developing fungal conidia. Conidia of the insect-pathogenic fungus Metarhizium robertsii were produced on potato dextrose agar (PDA) medium under normoxia (control = normal oxygen concentrations), continuous hypoxia, and transient anoxia, as well as minimal medium under normoxia. The tolerance of the conidia produced under these different conditions was evaluated in relation to wet heat (heat stress), menadione (oxidative stress), potassium chloride (osmotic stress), UV radiation, and 4-nitroquinoline-1-oxide (=4-NQO genotoxic stress). Growth under hypoxic condition induced higher conidial tolerance of M. robertsii to menadione, KCl, and UV radiation. Transient anoxic condition induced higher conidial tolerance to KCl and UV radiation. Nutritional stress (i.e., minimal medium) induced higher conidial tolerance to heat, menadione, KCl, and UV radiation. However, neither of these treatments induced higher tolerance to 4-NQO. The gene hsp30 and hsp101 encoding a heat shock protein was upregulated under anoxic condition. In conclusion, growth under hypoxia and anoxia produced conidia with higher stress tolerances than conidia produced in normoxic condition. The nutritive stress generated by minimal medium, however, induced much higher stress tolerances. This condition also caused the highest level of gene expression in the hsp30 and hsp101 genes. Thus, the conidia produced under nutritive stress, hypoxia, and anoxia had greater adaptation to stress.
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Affiliation(s)
| | - Nicolás Pedrini
- Instituto de Investigaciones Bioquímicas de La Plata (CONICET CCT La Plata-UNLP), Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - Breno Pupin
- Centro de Ciência do Sistema Terrestre, Instituto Nacional de Pesquisa Espaciais - INPE, São José dos Campos, SP, 12227-010, Brazil
| | - Donald W Roberts
- Department of Biology, Utah State University, Logan, UT, 84322-5305, USA
| | - Drauzio E N Rangel
- Universidade Tecnológica Federal do Paraná (UTFPR), 85660-000, Dois Vizinhos, PR, Brazil.
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42
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Li GQ, Xia J, Zeng W, Luo W, Liu L, Zeng X, Cao D. The intestinal γδ T cells: functions in the gut and in the distant organs. Front Immunol 2023; 14:1206299. [PMID: 37398661 PMCID: PMC10311558 DOI: 10.3389/fimmu.2023.1206299] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023] Open
Abstract
Located in the frontline against the largest population of microbiota, the intestinal mucosa of mammals has evolved to become an effective immune system. γδ T cells, a unique T cell subpopulation, are rare in circulation blood and lymphoid tissues, but rich in the intestinal mucosa, particularly in the epithelium. Via rapid production of cytokines and growth factors, intestinal γδ T cells are key contributors to epithelial homeostasis and immune surveillance of infection. Intriguingly, recent studies have revealed that the intestinal γδ T cells may play novel exciting functions ranging from epithelial plasticity and remodeling in response to carbohydrate diets to the recovery of ischemic stroke. In this review article, we update regulatory molecules newly defined in lymphopoiesis of the intestinal γδ T cells and their novel functions locally in the intestinal mucosa, such as epithelial remodeling, and distantly in pathological setting, e.g., ischemic brain injury repair, psychosocial stress responses, and fracture repair. The challenges and potential revenues in intestinal γδ T cell studies are discussed.
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Affiliation(s)
- Guo-Qing Li
- Department of Gastroenterology, Clinical Research Center, the Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Hunan Provincial Key Laboratory of Basic and Clinical Pharmacological Research on Gastrointestinal Tumors, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Jiliang Xia
- Hunan Province Key Laboratory of Cancer Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Weihong Zeng
- Hunan Province Key Laboratory of Cancer Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Weijia Luo
- Hunan Province Key Laboratory of Cancer Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Logen Liu
- Hunan Provincial Key Laboratory of Basic and Clinical Pharmacological Research on Gastrointestinal Tumors, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Xi Zeng
- Hunan Province Key Laboratory of Cancer Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Deliang Cao
- Department of Gastroenterology, Clinical Research Center, the Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Hunan Province Key Laboratory of Cancer Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Department of Oncology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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43
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Bayram ÖS, Bayram Ö. An Anatomy of Fungal Eye: Fungal Photoreceptors and Signalling Mechanisms. J Fungi (Basel) 2023; 9:jof9050591. [PMID: 37233302 DOI: 10.3390/jof9050591] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023] Open
Abstract
Organisms have developed different features to capture or sense sunlight. Vertebrates have evolved specialized organs (eyes) which contain a variety of photosensor cells that help them to see the light to aid orientation. Opsins are major photoreceptors found in the vertebrate eye. Fungi, with more than five million estimated members, represent an important clade of living organisms which have important functions for the sustainability of life on our planet. Light signalling regulates a range of developmental and metabolic processes including asexual sporulation, sexual fruit body formation, pigment and carotenoid production and even production of secondary metabolites. Fungi have adopted three groups of photoreceptors: (I) blue light receptors, White Collars, vivid, cryptochromes, blue F proteins and DNA photolyases, (II) red light sensors, phytochromes and (III) green light sensors and microbial rhodopsins. Most mechanistic data were elucidated on the roles of the White Collar Complex (WCC) and the phytochromes in the fungal kingdom. The WCC acts as both photoreceptor and transcription factor by binding to target genes, whereas the phytochrome initiates a cascade of signalling by using mitogen-activated protein kinases to elicit its cellular responses. Although the mechanism of photoreception has been studied in great detail, fungal photoreception has not been compared with vertebrate vision. Therefore, this review will mainly focus on mechanistic findings derived from two model organisms, namely Aspergillus nidulans and Neurospora crassa and comparison of some mechanisms with vertebrate vision. Our focus will be on the way light signalling is translated into changes in gene expression, which influences morphogenesis and metabolism in fungi.
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Affiliation(s)
| | - Özgür Bayram
- Biology Department, Maynooth University, W23 F2K8 Maynooth, Co. Kildare, Ireland
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44
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Haq IU, Mukhtar Z, Anwar-Ul-Haq M, Liaqat S. Deciphering host-pathogen interaction during Streptomyces spp. infestation of potato. Arch Microbiol 2023; 205:222. [PMID: 37149838 DOI: 10.1007/s00203-023-03560-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/08/2023]
Abstract
Potato crop, currently, is the staple food crop of about 1.3 billion global population. Potato is attaining even more admiration globally day by day owing to its public acceptability. However, potato sustainable production is distinctly challenged by multiple factors like diseases, pests and climate change etc. Among diseases, common scab is one of the prime threats to potato crop due to its soil-borne nature and versatility in phytotoxins' secretion. Common scab is caused multiple number of phytopathogenic streptomyces strains. Despite extensive research programs, researchers are still unable to identify a significant solution to this threat that is proliferating exceptional rate across the globe. To develop feasible remedies, adequate information regarding host-pathogen interaction should be available. This review possesses insights on existing pathogenic species, the evolution of novel pathogenic streptomyces spp. and phytotoxins produced by the pathogenic strains. Furthermore, which type of physiological, biochemical and genetic activities occur during pathogen's infestation of the host are also canvassed.
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Affiliation(s)
- Ihtisham Ul Haq
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.
- Ayub Agricultural Research Institute, Faisalabad, Pakistan.
| | - Zahid Mukhtar
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | | | - Sana Liaqat
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
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45
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Vasconcelos L, Aburjaile F, Andrade L, Cancio AF, Seyffert N, Aguiar ERGR, Ristow P. Genomic insights into the c-di-GMP signaling and biofilm development in the saprophytic spirochete Leptospira biflexa. Arch Microbiol 2023; 205:180. [PMID: 37031284 DOI: 10.1007/s00203-023-03519-7] [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: 10/01/2022] [Revised: 03/20/2023] [Accepted: 03/26/2023] [Indexed: 04/10/2023]
Abstract
C-di-GMP is a bacterial second messenger with central role in biofilm formation. Spirochete bacteria from Leptospira genus present a wide diversity, with species of medical importance and environmental species, named as saprophytic. Leptospira form biofilms in the rat's reservoir kidneys and in the environment. Here, we performed genomic analyses to identify enzymatic and effector c-di-GMP proteins in the saprophytic biofilm-forming species Leptospira biflexa serovar Patoc. We identified 40 proteins through local alignments. Amongst them, 16 proteins are potentially functional diguanylate cyclases, phosphodiesterases, or hybrid proteins. We also identified nine effectors, including PilZ proteins. Enrichment analyses suggested that c-di-GMP interacts with cAMP signaling system, CsrA system, and flagella assembly regulation during biofilm development of L. biflexa. Finally, we identified eight proteins in the pathogen Leptospira interrogans serovar Copenhageni that share high similarity with L. biflexa c-di-GMP-related proteins. This work revealed proteins related to c-di-GMP turnover and cellular response in Leptospira and their potential roles during biofilm development.
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Affiliation(s)
- Larissa Vasconcelos
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Flávia Aburjaile
- Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lara Andrade
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil
| | | | - Núbia Seyffert
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil
- Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Eric R G R Aguiar
- Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
- Department of Biological Science, Center of Biotechnology and Genetics, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | - Paula Ristow
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil.
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Federal University of Bahia, Salvador, Bahia, Brazil.
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46
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Salminen A. Aryl hydrocarbon receptor (AhR) impairs circadian regulation: impact on the aging process. Ageing Res Rev 2023; 87:101928. [PMID: 37031728 DOI: 10.1016/j.arr.2023.101928] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/23/2023] [Accepted: 04/06/2023] [Indexed: 04/11/2023]
Abstract
Circadian clocks control the internal sleep-wake rhythmicity of 24hours which is synchronized by the solar cycle. Circadian regulation of metabolism evolved about 2.5 billion years ago, i.e., the rhythmicity has been conserved from cyanobacteria and Archaea through to mammals although the mechanisms utilized have developed with evolution. While the aryl hydrocarbon receptor (AhR) is an evolutionarily conserved defence mechanism against environmental threats, it has gained many novel functions during evolution, such as the regulation of cell cycle, proteostasis, and many immune functions. There is robust evidence that AhR signaling impairs circadian rhythmicity, e.g., by interacting with the core BMAL1/CLOCK complex and disturbing the epigenetic regulation of clock genes. The maintenance of circadian rhythms is impaired with aging, disturbing metabolism and many important functions in aged organisms. Interestingly, it is known that AhR signaling promotes an age-related tissue degeneration, e.g., it is able to inhibit autophagy, enhance cellular senescence, and disrupt extracellular matrix. These alterations are rather similar to those induced by a long-term impairment of circadian rhythms. However, it is not known whether AhR signaling enhances the aging process by impairing circadian homeostasis. I will examine the experimental evidence indicating that AhR signaling is able to promote the age-related degeneration via a disruption of circadian rhythmicity.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
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Sanchez L, Epps J, Wall S, McQueen C, Pearson SJ, Scribner K, Wellberg EA, Giles ED, Rijnkels M, Porter WW. SIM2s directed Parkin-mediated mitophagy promotes mammary epithelial cell differentiation. Cell Death Differ 2023:10.1038/s41418-023-01146-9. [PMID: 36966227 DOI: 10.1038/s41418-023-01146-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/27/2023] Open
Abstract
The functionally differentiated mammary gland adapts to extreme levels of stress from increased demand for energy by activating specific protective mechanisms to support neonatal health. Here, we identify the breast tumor suppressor gene, single-minded 2 s (SIM2s) as a novel regulator of mitophagy, a key component of this stress response. Using tissue-specific mouse models, we found that loss of Sim2 reduced lactation performance, whereas gain (overexpression) of Sim2s enhanced and extended lactation performance and survival of mammary epithelial cells (MECs). Using an in vitro model of MEC differentiation, we observed SIM2s is required for Parkin-mediated mitophagy, which we have previously shown as necessary for functional differentiation. Mechanistically, SIM2s localizes to mitochondria to directly mediate Parkin mitochondrial loading. Together, our data suggest that SIM2s regulates the rapid recycling of mitochondria via mitophagy, enhancing the function and survival of differentiated MECs.
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Affiliation(s)
- Lilia Sanchez
- Department of Veterinary Physiology and Pharmacology; College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Jessica Epps
- Department of Veterinary Physiology and Pharmacology; College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Steven Wall
- Department of Veterinary Physiology and Pharmacology; College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Cole McQueen
- Department of Veterinary Physiology and Pharmacology; College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Scott J Pearson
- Department of Veterinary Physiology and Pharmacology; College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Kelly Scribner
- Department of Toxicology, CTEH, 5120 Northshore Drive, Little Rock, AR, 72118, USA
| | - Elizabeth A Wellberg
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Erin D Giles
- School of Kinesiology, University of Michigan, 830 N University Ave, Ann Arbor, MI, 48109, USA
| | - Monique Rijnkels
- Department of Veterinary Integrative Biosciences; College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
| | - Weston W Porter
- Department of Veterinary Physiology and Pharmacology; College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
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Wang F, Yang Z, Li J, Ma Y, Tu Y, Zeng X, Wang Q, Jiang Y, Huang S, Yi Q. The involvement of hypoxia inducible factor-1α on the proportion of three types of haemocytes in Chinese mitten crab under hypoxia stress. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 140:104598. [PMID: 36511346 DOI: 10.1016/j.dci.2022.104598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Hypoxia triggers diverse cell physiological processes, and the hypoxia inducible factors (HIFs) are a family of heterodimeric transcription factors that function as master regulators to respond to hypoxia in different cells. However, the knowledge about the hypoxic responses especially cell alteration mediated by HIFs under hypoxia stress is still limited in crustaceans. In the present study, a hypoxia-inducible factor-1α (HIF-1α) gene was identified (designed as EsHIF-1α). The relative mRNA expression level of EsHIF-1α was highest in hyalinocytes and lowest in granulocytes among three types of haemocytes in crabs. Hypoxia could significantly increase the EsHIF-1α protein expression level in haemocytes. Meanwhile, the proportion of hyalinocytes began to increase from 3 h post hypoxia treatment, and reached the highest level at 24 h. However, the opposite variation in proportion of granulocytes was observed under hypoxia stress. Further investigation showed that the inhibition of EsHIF-1α induced by KC7F2 (HIF-1α inhibitor) could lead to the significant decrease in the proportion of hyalinocytes under hypoxia stress, and also resulted in an increase of granulocytes proportion. While, after EsHIF-1α was activated by IOX4 (HIF-1α activator), the proportion of hyalinocytes was significantly up-regulated and the proportion of granulocytes was significantly down-regulated under post hypoxia treatment. These results collectively suggested that EsHIF-1α was involved in the regulation of proportion of three types of haemocytes induced by hypoxia stress, which provided vital insight into the understanding of the crosstalk between hypoxia and cell development in invertebrates.
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Affiliation(s)
- Fengchi Wang
- College of Aquaculture and Life Science, Dalian Ocean University, Dalian, 11026, China
| | - Zhichao Yang
- College of Aquaculture and Life Science, Dalian Ocean University, Dalian, 11026, China
| | - Jiaming Li
- College of Aquaculture and Life Science, Dalian Ocean University, Dalian, 11026, China
| | - Yuhan Ma
- College of Aquaculture and Life Science, Dalian Ocean University, Dalian, 11026, China
| | - Yuhan Tu
- College of Aquaculture and Life Science, Dalian Ocean University, Dalian, 11026, China
| | - Xiaorui Zeng
- College of Aquaculture and Life Science, Dalian Ocean University, Dalian, 11026, China
| | - Qingyao Wang
- College of Aquaculture and Life Science, Dalian Ocean University, Dalian, 11026, China
| | - Yusheng Jiang
- College of Aquaculture and Life Science, Dalian Ocean University, Dalian, 11026, China
| | - Shu Huang
- College of Aquaculture and Life Science, Dalian Ocean University, Dalian, 11026, China.
| | - Qilin Yi
- College of Aquaculture and Life Science, Dalian Ocean University, Dalian, 11026, China.
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Schmitz JM, Wolters JF, Murray NH, Guerra RM, Bingman CA, Hittinger CT, Pagliarini DJ. Aim18p and Aim46p are chalcone isomerase domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae. J Biol Chem 2023; 299:102981. [PMID: 36739946 PMCID: PMC9996372 DOI: 10.1016/j.jbc.2023.102981] [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: 11/15/2022] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Chalcone isomerases (CHIs) have well-established roles in the biosynthesis of plant flavonoid metabolites. Saccharomyces cerevisiae possesses two predicted CHI-like proteins, Aim18p (encoded by YHR198C) and Aim46p (YHR199C), but it lacks other enzymes of the flavonoid pathway, suggesting that Aim18p and Aim46p employ the CHI fold for distinct purposes. Here, we demonstrate using proteinase K protection assays, sodium carbonate extractions, and crystallography that Aim18p and Aim46p reside on the mitochondrial inner membrane and adopt CHI folds, but they lack select active site residues and possess an extra fungal-specific loop. Consistent with these differences, Aim18p and Aim46p lack CHI activity and also the fatty acid-binding capabilities of other CHI-like proteins, but instead bind heme. We further show that diverse fungal homologs also bind heme and that Aim18p and Aim46p possess structural homology to a bacterial hemoprotein. Collectively, our work reveals a distinct function and cellular localization for two CHI-like proteins, introduces a new variation of a hemoprotein fold, and suggests that ancestral CHI-like proteins were hemoproteins.
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Affiliation(s)
- Jonathan M Schmitz
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA
| | - John F Wolters
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nathan H Murray
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Rachel M Guerra
- Morgridge Institute for Research, Madison, Wisconsin, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, USA; Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA.
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50
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Mansour M, Abou-Aisha K. regO: a novel locus in the regulation of tetrapyrrole biosynthesis in Rhodospirillum rubrum. ANN MICROBIOL 2023. [DOI: 10.1186/s13213-022-01709-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Abstract
Purpose
A new locus, regO, involved in the regulation of photosynthesis gene expression in response to oxygen and light, has been studied in Rhodosprillum rubrum ATCC1117 (Rsp. rubrum) for identification of its function.
Methods
Inactivation of regO by interposon mutagenesis resulted in the inability of cells to grow photosynthetically, (i.e. become PS–). Protein domain analysis of RegO using the BLAST engine was also performed.
Results
The mutant strain was able to grow only anaerobically in the dark in the presence of DMSO as an external electron acceptor. Under these conditions, the mutant strain produced substantially lower amounts of photosynthetic membranes, indicating that regO is involved in the regulation of photosynthetic gene expression in response to anaerobiosis. The Rsp. rubrum REGO–disrupted mutant recovered the synthesis of photosynthetic membranes and retained regulation by light and/or oxygen tension when wild-type regO was provided in-trans.
Protein domain analysis of RegO revealed that it encodes a multi-domain sensor histidine kinase (HK). The signal-input domains, or PAS domains, bear strong similarities to putative heme-bound sensors involved in sensing light, redox potential, and/or oxygen. The output HK domain exhibits strong homology to sensor domains from bacterial two-component systems involved in signal transduction in response to the same environmental signals.
Conclusion
regO is coding for a sensor histidine kinase that belongs to bacterial two-component systems responsible for signal transduction in response to light and oxygen, particularly in the absence of oxygen. It is believed to be involved in the regulation of tetrapyrrole biosynthesis, which was shown as a lack of photosynthetic membranes in the mutant strain REGO– .Unlike other sensor kinase homologues from related anoxygenic phototrophic bacterial species, although functionally similar to RegB and PrrB, RegO is predicted to lack transmembrane domains and is thus expected to be a cytosolic member of a two-component signal transduction system. RegO also differs from its functional homologues, Reg B/PrrB sensor protein kinases, of the two component systems in that it lacks the second component of this two-component signal transduction system found in the neighboring genes. That encouraged us to give it the name RegO, indicating the lack of a cognate response regulator similar to Reg A/PrrA on other closely related anoxygenic Rhodobacter species.
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