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Ye J, Zhuang M, Hong M, Zhang D, Ren G, Hu A, Yang C, He Z, Zhou S. Methanogenesis in the presence of oxygenic photosynthetic bacteria may contribute to global methane cycle. Nat Commun 2024; 15:5682. [PMID: 38971854 PMCID: PMC11227571 DOI: 10.1038/s41467-024-50108-3] [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: 01/20/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024] Open
Abstract
Accumulating evidences are challenging the paradigm that methane in surface water primarily stems from the anaerobic transformation of organic matters. Yet, the contribution of oxygenic photosynthetic bacteria, a dominant species in surface water, to methane production remains unclear. Here we show methanogenesis triggered by the interaction between oxygenic photosynthetic bacteria and anaerobic methanogenic archaea. By introducing cyanobacterium Synechocystis PCC6803 and methanogenic archaea Methanosarcina barkeri with the redox cycling of iron, CH4 production was induced in coculture biofilms through both syntrophic methanogenesis (under anoxic conditions in darkness) and abiotic methanogenesis (under oxic conditions in illumination) during the periodic dark-light cycles. We have further demonstrated CH4 production by other model oxygenic photosynthetic bacteria from various phyla, in conjunction with different anaerobic methanogenic archaea exhibiting diverse energy conservation modes, as well as various common Fe-species. These findings have revealed an unexpected link between oxygenic photosynthesis and methanogenesis and would advance our understanding of photosynthetic bacteria's ecological role in the global CH4 cycle. Such light-driven methanogenesis may be widely present in nature.
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Affiliation(s)
- Jie Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Minghan Zhuang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingqiu Hong
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dong Zhang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guoping Ren
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Andong Hu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chaohui Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhen He
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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2
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Patyi G, Hódi B, Mallick I, Maróti G, Kós PB, Vass I. Investigation of singlet-oxygen-responsive genes in the cyanobacterium Synechocystis PCC 6803. PHYSIOLOGIA PLANTARUM 2024; 176:e14468. [PMID: 39140254 DOI: 10.1111/ppl.14468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 07/08/2024] [Accepted: 07/23/2024] [Indexed: 08/15/2024]
Abstract
Singlet oxygen (1O2) is an important reactive oxygen species whose formation by the type-II, light-dependent, photodynamic reaction is inevitable during photosynthetic processes. In the last decades, the recognition that 1O2 is not only a damaging agent, but can also affect gene expression and participates in signal transduction pathways has received increasing attention. However, contrary to several other taxa, 1O2-responsive genes have not been identified in the important cyanobacterial model organism Synechocystis PCC 6803. By using global transcript analysis we have identified a large set of Synechocystis genes, whose transcript levels were either enhanced or repressed in the presence of 1O2. Characteristic 1O2 responses were observed in several light-inducible genes of Synechocystis, especially in the hli (or scp) family encoding HLIP/SCP proteins involved in photoprotection. Other important 1O2-induced genes include components of the Photosystem II repair machinery (psbA2 and ftsH2, ftsH3), iron homeostasis genes isiA and idiA, the group 2 sigma factor sigD, some components of the transcriptomes induced by salt-, hyperosmotic and cold-stress, as well as several genes of unknown function. The most pronounced 1O2-induced upregulation was observed for the hliB and the co-transcribed lilA genes, whose deletion induced enhanced sensitivity against 1O2-mediated light damage. A bioreporter Synechocystis strain was created by fusing the hliB promoter to the bacterial luciferase (lux), which showed its utility for continuous monitoring of 1O2 concentrations inside the cell.
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Affiliation(s)
- Gábor Patyi
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
- Faculty of Science and Informatics, Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Barbara Hódi
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
- Faculty of Science and Informatics, Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Ivy Mallick
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Péter B Kós
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, Faculty of Science and Informatics, University of Szeged, Hungary
| | - Imre Vass
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
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3
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Sivasubramaniam BP, Washer BM, Watanabe Y, Ragheb KE, Robinson JP, Wei A. Photodynamic treatment of Staphylococcus aureus with non-iron hemin analogs in the presence of hydrogen peroxide. RSC Med Chem 2024; 15:2138-2145. [PMID: 38911164 PMCID: PMC11187572 DOI: 10.1039/d4md00148f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/02/2024] [Indexed: 06/25/2024] Open
Abstract
Bacteria subjected to antiseptic or antibiotic stress often develop tolerance, a trait that can lead to permanent resistance. To determine whether photodynamic agents could be used to counter tolerance, we evaluated three non-iron hemin analogs (M-PpIX; M = Al, Ga, In) as targeted photosensitizers for antimicrobial photodynamic inactivation (aPDI) following exposure to sublethal H2O2. Al-PpIX is an active producer of ROS whereas Ga- and In-PpIX are more efficient at generating singlet oxygen. Al- and Ga-PpIX are highly potent aPDI agents against S. aureus and methicillin-resistant strains (MRSA) with antimicrobial activity (3 log reduction in colony-forming units) at nanomolar concentrations. The aPDI activities of Al- and Ga-PpIX against S. aureus were tested in the presence of 1 mM H2O2 added at different stages of growth. Bacteria exposed to H2O2 during log-phase growth were less susceptible to aPDI but bacteria treated with H2O2 in their postgrowth phase exhibited aPDI hypersensitivity, with no detectable colony growth after treatment with 15 nM Ga-PpIX.
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Affiliation(s)
| | - Benjamin M Washer
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette IN 47907 USA
| | - Yuichiro Watanabe
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette IN 47907 USA
| | - Kathryn E Ragheb
- College of Veterinary Medicine, Purdue University 625 Harrison Street West Lafayette IN 47907 USA
| | - J Paul Robinson
- College of Veterinary Medicine, Purdue University 625 Harrison Street West Lafayette IN 47907 USA
| | - Alexander Wei
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette IN 47907 USA
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4
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Kretz J, Börner J, Friedrich T, McIntosh M, Procida-Kowalski T, Gerken F, Wilhelm J, Klug G. Function of the RNA-targeting class 2 type VI CRISPR Cas system of Rhodobacter capsulatus. Front Microbiol 2024; 15:1384543. [PMID: 38741736 PMCID: PMC11089165 DOI: 10.3389/fmicb.2024.1384543] [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: 02/09/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Bacteria use CRISPR Cas systems to defend against invading foreign nucleic acids, e.g., phage genomes, plasmids or mobile genetic elements. Some CRISPR Cas systems were reported to have physiological importance under a variety of abiotic stress conditions. We used physiological tests under different stress conditions and RNA-seq analyses to address the possible function of the RNA-targeting class 2 type VI CRISPR Cas system of the facultative phototrophic α-proteobacterium Rhodobacter capsulatus. Expression of the system was low under exponential non-stress conditions and high during oxidative stress, membrane stress and in stationary phase. Induction of the CRISPR Cas system in presence of a target protospacer RNA resulted in a growth arrest of R. capsulatus. RNA-seq revealed a strong alteration of the R. capsulatus transcriptome when cas13a was induced in presence of a target protospacer. RNA 5' end mapping indicated that the CRISPR Cas-dependent transcriptome remodeling is accompanied by fragmentation of cellular RNAs, e.g., for mRNAs originating from a genomic locus which encodes multiple ribosomal proteins and the RNA polymerase subunits RpoA, RpoB and RpoC. The data suggest a function of this CRISPR Cas system in regulated growth arrest, which may prevent the spread of phages within the population.
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Affiliation(s)
- Jonas Kretz
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | - Janek Börner
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | - Tobias Friedrich
- Institute of Biochemistry, Justus-Liebig-University, Giessen, Germany
- Biomedical Informatics and Systems Medicine, Justus-Liebig-University, Giessen, Germany
| | - Matthew McIntosh
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | | | - Florian Gerken
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | - Jochen Wilhelm
- Institute for Lung Health, Justus-Liebig-University, Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
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Tinguely C, Paulméry M, Terrettaz C, Gonzalez D. Diurnal cycles drive rhythmic physiology and promote survival in facultative phototrophic bacteria. ISME COMMUNICATIONS 2023; 3:125. [PMID: 38001234 PMCID: PMC10674011 DOI: 10.1038/s43705-023-00334-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023]
Abstract
Bacteria have evolved many strategies to spare energy when nutrients become scarce. One widespread such strategy is facultative phototrophy, which helps heterotrophs supplement their energy supply using light. Our knowledge of the impact that such behaviors have on bacterial fitness and physiology is, however, still limited. Here, we study how a representative of the genus Porphyrobacter, in which aerobic anoxygenic phototrophy is ancestral, responds to different light regimes under nutrient limitation. We show that bacterial survival in stationary phase relies on functional reaction centers and varies depending on the light regime. Under dark-light alternance, our bacterial model presents a diphasic life history dependent on phototrophy: during dark phases, the cells inhibit DNA replication and part of the population lyses and releases nutrients, while subsequent light phases allow for the recovery and renewed growth of the surviving cells. We correlate these cyclic variations with a pervasive pattern of rhythmic transcription which reflects global changes in diurnal metabolic activity. Finally, we demonstrate that, compared to either a phototrophy mutant or a bacteriochlorophyll a overproducer, the wild type strain is better adapted to natural environments, where regular dark-light cycles are interspersed with additional accidental dark episodes. Overall, our results highlight the importance of light-induced biological rhythms in a new model of aerobic anoxygenic phototroph representative of an ecologically important group of environmental bacteria.
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Affiliation(s)
- Camille Tinguely
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Mélanie Paulméry
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Céline Terrettaz
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Diego Gonzalez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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Huang BC, Li GF, Ren ZQ, Ji XM, Wang Y, Gu YN, Li JP, Chang RR, Fan NS, Jin RC. Light-Driven Electron Uptake from Nonfermentative Organic Matter to Expedite Nitrogen Dissimilation by Chemolithotrophic Anammox Consortia. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12732-12740. [PMID: 37590181 DOI: 10.1021/acs.est.3c04160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Nonphotosynthetic microorganisms are typically unable to directly utilize light energy, but light might change the metabolic pathway of these bacteria indirectly by forming intermediates such as reactive oxygen species (ROS). This work investigated the role of light on nitrogen conversion by anaerobic ammonium oxidation (anammox) consortia. The results showed that high intensity light (>20000 lx) caused ca. 50% inhibition of anammox activity, and total ROS reached 167% at 60,000 lx. Surprisingly, 200 lx light was found to induce unexpected promotion of the nitrogen conversion rate, and ultraviolet light (<420 nm) was identified as the main contributor. Metagenomic and metatranscriptomic analyses revealed that the gene encoding cytochrome c peroxidase was highly expressed only under 200 lx light. 15N isotope tracing, gene abundance quantification, and external H2O2 addition experiments showed that photoinduced trace H2O2 triggered cytochrome c peroxidase expression to take up electrons from extracellular nonfermentative organics to synthesize NADH and ATP, thereby expediting nitrogen dissimulation of anammox consortia. External supplying reduced humic acid into a low-intensity light exposure system would result in a maximal 1.7-fold increase in the nitrogen conversion rate. These interesting findings may provide insight into the niche differentiation and widespread nature of anammox bacteria in natural ecotopes.
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Affiliation(s)
- Bao-Cheng Huang
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Gui-Feng Li
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Zhi-Qi Ren
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Xiao-Ming Ji
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ye Wang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ye-Nan Gu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Jing-Peng Li
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Rong-Rong Chang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Nian-Si Fan
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ren-Cun Jin
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
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7
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Ku RH, Li LH, Liu YF, Hu EW, Lin YT, Lu HF, Yang TC. Implication of the σ E Regulon Members OmpO and σ N in the Δ ompA299-356-Mediated Decrease of Oxidative Stress Tolerance in Stenotrophomonas maltophilia. Microbiol Spectr 2023; 11:e0108023. [PMID: 37284772 PMCID: PMC10433810 DOI: 10.1128/spectrum.01080-23] [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: 03/13/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023] Open
Abstract
Outer membrane protein A (OmpA) is the most abundant porin in bacterial outer membranes. KJΔOmpA299-356, an ompA C-terminal in-frame deletion mutant of Stenotrophomonas maltophilia KJ, exhibits pleiotropic defects, including decreased tolerance to menadione (MD)-mediated oxidative stress. Here, we elucidated the underlying mechanism of the decreased MD tolerance mediated by ΔompA299-356. The transcriptomes of wild-type S. maltophilia and the KJΔOmpA299-356 mutant strain were compared, focusing on 27 genes known to be associated with oxidative stress alleviation; however, no significant differences were identified. OmpO was the most downregulated gene in KJΔOmpA299-356. KJΔOmpA299-356 complementation with the chromosomally integrated ompO gene restored MD tolerance to the wild-type level, indicating the role of OmpO in MD tolerance. To further clarify the possible regulatory circuit involved in ompA defects and ompO downregulation, σ factor expression levels were examined based on the transcriptome results. The expression levels of three σ factors were significantly different (downregulated levels of rpoN and upregulated levels of rpoP and rpoE) in KJΔOmpA299-356. Next, the involvement of the three σ factors in the ΔompA299-356-mediated decrease in MD tolerance was evaluated using mutant strains and complementation assays. rpoN downregulation and rpoE upregulation contributed to the ΔompA299-356-mediated decrease in MD tolerance. OmpA C-terminal domain loss induced an envelope stress response. Activated σE decreased rpoN and ompO expression levels, in turn decreasing swimming motility and oxidative stress tolerance. Finally, we revealed both the ΔompA299-356-rpoE-ompO regulatory circuit and rpoE-rpoN cross regulation. IMPORTANCE The cell envelope is a morphological hallmark of Gram-negative bacteria. It consists of an inner membrane, a peptidoglycan layer, and an outer membrane. OmpA, an outer membrane protein, is characterized by an N-terminal β-barrel domain that is embedded in the outer membrane and a C-terminal globular domain that is suspended in the periplasmic space and connected to the peptidoglycan layer. OmpA is crucial for the maintenance of envelope integrity. Stress resulting from the destruction of envelope integrity is sensed by extracytoplasmic function (ECF) σ factors, which induce responses to various stressors. In this study, we revealed that loss of the OmpA-peptidoglycan (PG) interaction causes peptidoglycan and envelope stress while simultaneously upregulating σP and σE expression levels. The outcomes of σP and σE activation are different and are linked to β-lactam and oxidative stress tolerance, respectively. These findings establish that outer membrane proteins (OMPs) play a critical role in envelope integrity and stress tolerance.
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Affiliation(s)
- Ren-Hsuan Ku
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Li-Hua Li
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yi-Fu Liu
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - En-Wei Hu
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Tsung Lin
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsu-Feng Lu
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan
| | - Tsuey-Ching Yang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
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Wu Y, Wang Y, Zhang Q, Chen T, Zhang C. BP@Au undergoes rapid degradation and releases singlet oxygen under dark conditions: Doping effect and detrimental effects on superoxide-producing marine algae. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131502. [PMID: 37121040 DOI: 10.1016/j.jhazmat.2023.131502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/02/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023]
Abstract
Black phosphorus (BP) shows encouraging utility in many fields, and metal doping has been suggested as an efficient way to improve stability. However, controversial results and inconsistent mechanisms have been reported for doping modulation and stability change. We observed the unforeseen evolution of singlet oxygen (1O2) from BP integrated with gold nanoparticles (BP@Au) under dark conditions, and this led to rapid BP deterioration, even though enhanced stability is commonly thought via surface doping. Briefly, the BP reacted with oxygen and water to yield superoxide (O2•-) and hydrogen peroxide. Au0 acted as an enzyme mimic and catalyzed the conversion of these derivatives, and Au0 was converted to a mixture of Au3+ and Au+. The O2•- was converted to 1O2 via direct donation of electrons to the Au3+/+. The Au-catalyzed redox reactions accelerated the degradation of the BP nanosheets. BP@Au showed significant toxicity toward marine alga that produce O2•- in the dark, as indicated by a more than 30% reduction in cell viability after 12 h of incubation with 7.56 mg/L BP@Au. The novelty of this work lies in the demonstration of a dopant-related degradation pathway of BP that shows unrevealed toxicity toward O2•--producing marine algae.
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Affiliation(s)
- Yining Wu
- School of Environment, Beijing Normal University, Beijing 100857, China
| | - Yating Wang
- School of Environment, Beijing Normal University, Beijing 100857, China
| | - Qiurong Zhang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Tianmin Chen
- School of Environment, Beijing Normal University, Beijing 100857, China
| | - Chengdong Zhang
- School of Environment, Beijing Normal University, Beijing 100857, China.
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Expanding the genetic toolkit helps dissect a global stress response in the early-branching species Fusobacterium nucleatum. Proc Natl Acad Sci U S A 2022; 119:e2201460119. [PMID: 36161895 PMCID: PMC9546586 DOI: 10.1073/pnas.2201460119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fusobacterium nucleatum, long known as a common oral microbe, has recently garnered attention for its ability to colonize tissues and tumors elsewhere in the human body. Clinical and epidemiological research has now firmly established F. nucleatum as an oncomicrobe associated with several major cancer types. However, with the current research focus on host associations, little is known about gene regulation in F. nucleatum itself, including global stress-response pathways that typically ensure the survival of bacteria outside their primary niche. This is due to the phylogenetic distance of Fusobacteriota to most model bacteria, their limited genetic tractability, and paucity of known gene functions. Here, we characterize a global transcriptional stress-response network governed by the extracytoplasmic function sigma factor, σE. To this aim, we developed several genetic tools for this anaerobic bacterium, including four different fluorescent marker proteins, inducible gene expression, scarless gene deletion, and transcriptional and translational reporter systems. Using these tools, we identified a σE response partly reminiscent of phylogenetically distant Proteobacteria but induced by exposure to oxygen. Although F. nucleatum lacks canonical RNA chaperones, such as Hfq, we uncovered conservation of the noncoding arm of the σE response in form of the noncoding RNA FoxI. This regulatory small RNA acts as an mRNA repressor of several membrane proteins, thereby supporting the function of σE. In addition to the characterization of a global stress response in F. nucleatum, the genetic tools developed here will enable further discoveries and dissection of regulatory networks in this early-branching bacterium.
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10
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Manoil D, Parga A, Hellesen C, Khawaji A, Brundin M, Durual S, Özenci V, Fang H, Belibasakis GN. Photo-oxidative stress response and virulence traits are co-regulated in E. faecalis after antimicrobial photodynamic therapy. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 234:112547. [PMID: 36030693 DOI: 10.1016/j.jphotobiol.2022.112547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/23/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Knowledge of photo-oxidative stress responses in bacteria that survive antimicrobial photodynamic therapy (aPDT) is scarce. Whereas aPDT is attracting growing clinical interest, subsequent stress responses are crucial to evaluate as they may lead to the up-regulation of pathogenic traits. Here, we aimed to assess transcriptional responses to sublethal aPDT-stress and identify potential connections with virulence-related genes. Six Enterococcus faecalis strains were investigated; ATCC 29212, three dental root-canal isolates labelled UmID1, UmID2 and UmID3 and two vancomycin-resistant isolates labelled A1 and A2. TMPyP was employed as a photosensitiser. A viability dose-response curve to increasing concentrations of TMPyP was determined by culture plating. Differential expression of genes involved in oxidative stress responses (dps and hypR), general stress responses (dnaK, sigma-factorV and relA), virulence-related genes (ace, fsrC and gelE) and vancomycin-resistance (vanA) was assessed by reverse-transcription qPCR. TMPyP-mediated aPDT inactivated all strains with comparable efficiencies. TMPyP at 0.015 μM was selected to induce sublethal photo-oxidative stress. Despite heterogeneities in gene expression between strains, transcriptional profiles revealed up-regulations of transcripts dps, hypR as well as dnaK and sigma factorV after exposure to TMPyP alone and to light-irradiated TMPyP. Specifically, the alternative sigma factorV reached up to 39 ± 113-fold (median ± IQR) (p = 0.0369) in strain A2. Up-regulation of the quorum sensing operon, fsr, and its downstream virulence-related gelatinase gelE were also observed in strains ATCC-29212, A1, A2 and UmID3. Finally, photo-oxidative stress induced vanA-type vancomycin-resistance gene in both carrier isolates, reaching up to 3.3 ± 17-fold in strain A2 (p = 0.015). These findings indicate that, while aPDT successfully inactivates vancomycin-resistant and naïve strains of E. faecalis, subpopulations of surviving cells respond by co-ordinately up-regulating a network of genes involved in stress survival and virulence. This includes the induction of vancomycin-resistance genes in carrier isolates. These data may provide the mechanistic basis to circumvent bacterial responses and improve future clinical protocols.
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Affiliation(s)
- Daniel Manoil
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden; Division of Cariology and Endodontics, University Clinics of Dental Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
| | - Ana Parga
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden; Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Cecilia Hellesen
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Arwa Khawaji
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Malin Brundin
- Division of Endodontics, Department of Odontology, Umeå University, Umeå, Sweden
| | - Stéphane Durual
- Biomaterials Laboratory, Division of Fixed Prosthodontics and Biomaterials, University Clinics of Dental Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Volkan Özenci
- Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Karolinska Institute, Huddinge, Stockholm, Sweden
| | - Hong Fang
- Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Karolinska Institute, Huddinge, Stockholm, Sweden
| | - Georgios N Belibasakis
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
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11
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Lee YR, Lee WH, Lee SY, Lee J, Kim MS, Moon M, Park GW, Kim HS, Kim JI, Lee JS, Lee S. Regulation of Reactive Oxygen Species Promotes Growth and Carotenoid Production Under Autotrophic Conditions in Rhodobacter sphaeroides. Front Microbiol 2022; 13:847757. [PMID: 35295297 PMCID: PMC8920488 DOI: 10.3389/fmicb.2022.847757] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/07/2022] [Indexed: 11/26/2022] Open
Abstract
Industrial demand for capture and utilization using microorganisms to reduce CO2, a major cause of global warming, is significantly increasing. Rhodobacter sphaeroides is a suitable strain for the process of converting CO2 into high-value materials because it can accept CO2 and has various metabolic pathways. However, it has been mainly studied for heterotrophic growth that uses sugars and organic acids as carbon sources, not autotrophic growth. Here, we report that the regulation of reactive oxygen species is critical for growth when using CO2 as a sole carbon source in R. sphaeroides. In general, the growth rate is much slower under autotrophic conditions compared to heterotrophic conditions. To improve this, we performed random mutagenesis using N-methyl-N’-nitro-N-nitrosoguanidine (NTG). As a result, we selected the YR-1 strain with a maximum specific growth rate (μ) 1.44 day–1 in the early growth phase, which has a 110% faster growth rate compared to the wild-type. Based on the transcriptome analysis, it was confirmed that the growth was more sensitive to reactive oxygen species under autotrophic conditions. In the YR-1 mutant, the endogenous contents of H2O2 levels and oxidative damage were reduced by 33.3 and 42.7% in the cells, respectively. Furthermore, we measured that concentrations of carotenoids, which are important antioxidants. The total carotenoid is produced 9.63 g/L in the YR-1 mutant, suggesting that the production is 1.7-fold higher than wild-type. Taken together, our observations indicate that controlling ROS promotes cell growth and carotenoid production under autotrophic conditions.
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Affiliation(s)
- Yu Rim Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
- Interdisciplinary Program of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Won-Heong Lee
- Interdisciplinary Program of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Soo Youn Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
| | - Jiye Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
| | - Min-Sik Kim
- Energy Resources Upcycling Research Laboratory, Korea Institute of Energy Research, Daejeon, South Korea
| | - Myounghoon Moon
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
| | - Gwon Woo Park
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
| | - Hui Su Kim
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
- Department of Advanced Chemicals and Engineering, Chonnam National University, Gwangju, South Korea
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Jin-Suk Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
| | - Sangmin Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
- *Correspondence: Sangmin Lee,
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12
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Jin X, Yang Y, Cao H, Gao B, Zhao Z. Eco-phylogenetic analyses reveal divergent evolution of vitamin B 12 metabolism in the marine bacterial family 'Psychromonadaceae'. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:147-163. [PMID: 34921716 DOI: 10.1111/1758-2229.13036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Cobalamin (vitamin B12 ) is an essential micronutrient required by both prokaryotes and eukaryotes. Nevertheless, with high genetic and metabolic cost, de novo cobalamin biosynthesis is exclusive to a subset of prokaryotic taxa. Many Cyanobacterial and Archaeal taxa have been implicated in de novo cobalamin biosynthesis in epi- and mesopelagic ocean respectively. However, the contributions of Gammaproteobacteria particularly the family 'Psychromonadaceae' is largely unknown. Through phylo-pangenomic analyses using concatenated single-copy proteins and homologous gene clusters respectively, the phylogenies within 'Psychromonadaceae' recapitulate both their taxonomic delineations and environmental distributions. Moreover, uneven distribution of cobalamin de novo biosynthetic operon and cobalamin-dependent light-responsive regulon were observed, and of which the linkages to the environmental conditions where cobalamin availability and light regime can be varied respectively were discussed, suggesting the impacts of ecological divergence in shaping their disparate cobalamin-related metabolisms. Functional analysis demonstrated a varying degree of cobalamin dependency for both central metabolic processes and cobalamin-mediated light-responsive regulation, and underlying sequence characteristics of cis- and trans-regulatory elements were revealed. Our findings emphasized the potential roles of cobalamin in shaping the ecological distributions and driving the metabolic evolution in the marine bacterial family 'Psychromonadaceae', and have further implications for an improved understanding of nutritional interdependencies and community metabolism modulated by cobalamin.
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Affiliation(s)
- Xingkun Jin
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yaofang Yang
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Haihang Cao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Zhe Zhao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
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13
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Saggere RMS, Lee CWJ, Chan ICW, Durnford DG, Nedelcu AM. A life-history trade-off gene with antagonistic pleiotropic effects on reproduction and survival in limiting environments. Proc Biol Sci 2022; 289:20212669. [PMID: 35078364 PMCID: PMC8790358 DOI: 10.1098/rspb.2021.2669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Although life-history trade-offs are central to life-history evolution, their mechanistic basis is often unclear. Traditionally, trade-offs are understood in terms of competition for limited resources among traits within an organism, which could be mediated by signal transduction pathways at the level of cellular metabolism. Nevertheless, trade-offs are also thought to be produced as a consequence of the performance of one activity generating negative consequences for other traits, or the result of genes or pathways that simultaneously regulate two life-history traits in opposite directions (antagonistic pleiotropy), independent of resource allocation. Yet examples of genes with antagonistic effects on life-history traits are limited. This study provides direct evidence for a gene-RLS1, that is involved in increasing survival in nutrient-limiting environments at a cost to immediate reproduction in the single-celled photosynthetic alga, Chlamydomonas reinhardtii. Specifically, we show that RLS1 mutants are unable to properly suppress their reproduction in phosphate-deprived conditions. Although these mutants have an immediate reproductive advantage relative to the parental strain, their long-term survival is negatively affected. Our data suggest that RLS1 is a bona fide life-history trade-off gene that suppresses immediate reproduction and ensures survival by downregulating photosynthesis in limiting environments, as part of the general acclimation response to nutrient deprivation in photosynthetic organisms.
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Affiliation(s)
- Rani M. S. Saggere
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, New Brunswick, Canada E3B 5A3
| | - Christopher W. J. Lee
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, New Brunswick, Canada E3B 5A3
| | - Irina C. W. Chan
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, New Brunswick, Canada E3B 5A3
| | - Dion G. Durnford
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, New Brunswick, Canada E3B 5A3
| | - Aurora M. Nedelcu
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, New Brunswick, Canada E3B 5A3
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14
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McIntosh M, Köchling T, Latz A, Kretz J, Heinen S, Konzer A, Klug G. A major checkpoint for protein expression in Rhodobacter sphaeroides during heat stress response occurs at the level of translation. Environ Microbiol 2021; 23:6483-6502. [PMID: 34668288 DOI: 10.1111/1462-2920.15818] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 10/05/2021] [Indexed: 12/24/2022]
Abstract
Temperature above the physiological optimum is a stress condition frequently faced by bacteria in their natural environments. Here, we were interested in the correlation between levels of RNA and protein under heat stress. Changes in RNA and protein levels were documented in cultures of Rhodobacter sphaeroides using RNA sequencing, quantitative mass spectrometry, western blot analysis, in vivo [35 S] methionine-labelling and plasmid-borne reporter fusions. Changes in the transcriptome were extensive. Strikingly, the proteome remained unchanged except for very few proteins. Examples include a heat shock protein, a DUF1127 protein of unknown function and sigma factor proteins from leaderless transcripts. Insight from this study indicates that R. sphaeroides responds to heat stress by producing a broad range of transcripts while simultaneously preventing translation from nearly all of them, and that this selective production of protein depends on the untranslated region of the transcript. We conclude that measurements of transcript abundance are insufficient to understand gene regulation. Rather, translation can be an important checkpoint for protein expression under certain environmental conditions. Furthermore, during heat shock, regulation at the level of transcription might represent preparation for survival in an unpredictable environment while regulation at translation ensures production of only a few proteins.
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Affiliation(s)
- Matthew McIntosh
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Thorsten Köchling
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Anna Latz
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Jonas Kretz
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Sandra Heinen
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Anne Konzer
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Gabriele Klug
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
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15
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Wakao S, Niyogi KK. Chlamydomonas as a model for reactive oxygen species signaling and thiol redox regulation in the green lineage. PLANT PHYSIOLOGY 2021; 187:687-698. [PMID: 35237823 PMCID: PMC8491031 DOI: 10.1093/plphys/kiab355] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/13/2021] [Indexed: 05/15/2023]
Abstract
One-sentence summary: Advances in proteomic and transcriptomic studies have made Chlamydomonas a powerful research model in redox and reactive oxygen species regulation with unique and overlapping mechanisms with plants.
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Affiliation(s)
- Setsuko Wakao
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Author for communication: Senior author
| | - Krishna K. Niyogi
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
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16
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Han J, Yin Y, Xu D, Wang H, Yu S, Han D, Niu Y, Xu R. Growth inhibition and oxidative damage of Microcystis aeruginosa induced by aqueous extract of different submerged macrophytes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:53224-53238. [PMID: 34023990 DOI: 10.1007/s11356-021-14459-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
With the increasing eutrophication of the aquatic environments, cyanobacteria blooms caused certain damage to the animals and plants in the aquatic environments. In this experiment, two species were selected from six species of submerged macrophytes, the experimental conditions were changed to achieve the best inhibitory effect on Microcystis aeruginosa, and oxidative damage analysis was carried out. The experiment results demonstrated that the inhibition rate of Vallisneria natans and Ceratophyllum demersum was nearly 100% at the concentration of 3 g/L after 15 days of anaerobic soaking extract. In addition, the longer the soaking time of the two submerged macrophytes, the weaker the photosynthesis effect, and the lower the chlorophyll fluorescence parameters, the more obvious the inhibition effect on M. aeruginosa. Lipid peroxidation injury of M. aeruginosa could be reflected by malondialdehyde (MDA) concentration. The MDA concentration in the experimental group was significantly higher than the control group. Results showed that V. natans and C. demersum could induce oxidative damage in M. aeruginosa. It was also observed that the secondary metabolites produced by V. natans were mainly fatty acids (e.g., the oxidative acid was 6.92 w/%, and the successful acid was 9.85 w/%) which inhibited M. aeruginosa in gas chromatography-mass spectrometry (GC-MS). The main secondary metabolites in C. demersum were hydroxyl acids (e.g., the 4-hydroxy-3-methoxyphenylacetic acid was 24.33 w/%), which could inhibit the algae through allelopathy. This study provided reference for submerged macrophytes to inhibit M. aeruginosa under different conditions.
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Affiliation(s)
- Jinlong Han
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan, 063000, People's Republic of China
| | - Yue Yin
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan, 063000, People's Republic of China
- North China University of Science and Technology Affiliated Hospital, Tangshan, 063000, People's Republic of China
| | - Duo Xu
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan, 063000, People's Republic of China
| | - Hao Wang
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan, 063000, People's Republic of China.
| | - Shuang Yu
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan, 063000, People's Republic of China
| | - Dongyun Han
- College of Chemical Engineering, North China University of Science and Technology, Tangshan, 063000, People's Republic of China
| | - Yunxia Niu
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan, 063000, People's Republic of China
| | - Runyu Xu
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan, 063000, People's Republic of China
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17
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Role of a fasciclin domain protein in photooxidative stress and flocculation in Azospirillum brasilense Sp7. Res Microbiol 2021; 172:103875. [PMID: 34461275 DOI: 10.1016/j.resmic.2021.103875] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 11/22/2022]
Abstract
Fasciclin domain proteins (FDP) are found in all domains of life, but their biological role and regulation are not clearly understood. While studying the proteome of a mutant (Car1) of Azospirillum brasilense Sp7 with a Tn5 insertion in the gene encoding an anti-sigma factor (ChrR1), we found that FDP was maximally expressed. To study the biological role of this FDP, we inactivated fdp in A. brasilense Sp7 and in its Car1 mutant, which rendered them sensitive to methylene blue (MB) and toluidine blue (TB) in the presence of light. The transcription of fdp was also strongly upregulated by an ECF sigma factor (RpoE1) and photooxidative stress. The fdp null mutants of A. brasilense Sp7 and its Car1 mutant produced relatively fewer carotenoids and showed reduced flocculation. The reduced ability of fdp null mutants to flocculate was partly due to their reduced ability to produce carotenoids as inhibition of carotenoid synthesis by diphenylamine reduced their flocculation ability by 15-20%. Hence, FDP plays an important role in protecting A. brasilense Sp7 against photo-oxidative stress by supporting carotenoid accumulation and cell aggregation.
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18
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Lemke RAS, Olson SM, Morse K, Karlen SD, Higbee A, Beebe ET, Ralph J, Coon JJ, Fox BG, Donohue TJ. A bacterial biosynthetic pathway for methylated furan fatty acids. J Biol Chem 2020; 295:9786-9801. [PMID: 32434926 PMCID: PMC7380195 DOI: 10.1074/jbc.ra120.013697] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/14/2020] [Indexed: 12/26/2022] Open
Abstract
Fatty acids play many important roles in cells and also in industrial processes. Furan fatty acids (FuFAs) are present in the lipids of some plant, fish, and microbial species and appear to function as second messengers in pathways that protect cells from membrane-damaging agents. We report here the results of chemical, genetic, and synthetic biology experiments to decipher the biosynthesis of the monomethylated FuFA, methyl 9-(3-methyl-5-pentylfuran-2-yl) nonanoate (9M5-FuFA), and its dimethyl counterpart, methyl 9-(3,4-dimethyl-5-pentylfuran-2-yl) nonanoate (9D5-FuFA), in two α-proteobacteria. Each of the steps in FuFA biosynthesis occurs on pre-existing phospholipid fatty acid chains, and we identified pathway intermediates and the gene products that catalyze 9M5-FuFA and 9D5-FuFA synthesis in Rhodobacter sphaeroides 2.4.1 and Rhodopseudomonas palustris CGA009. One previously unknown pathway intermediate was a methylated diunsaturated fatty acid, (10E,12E)-11-methyloctadeca-10,12-dienoic acid (11Me-10t,12t-18:2), produced from (11E)-methyloctadeca-11-enoic acid (11Me-12t-18:1) by a newly identified fatty acid desaturase, UfaD. We also show that molecular oxygen (O2) is the source of the oxygen atom in the furan ring of 9M5-FuFA, and our findings predict that an O2-derived oxygen atom is incorporated into 9M5-FuFA via a protein, UfaO, that uses the 11Me-10t,12t-18:2 fatty acid phospholipid chain as a substrate. We discovered that R. palustris also contains a SAM-dependent methylase, FufM, that produces 9D5-FuFA from 9M5-FuFA. These results uncover the biochemical sequence of intermediates in a bacterial pathway for 9M5-FuFA and 9D5-FuFA biosynthesis and suggest the existence of homologs of the enzymes identified here that could function in FuFA biosynthesis in other organisms.
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Affiliation(s)
- Rachelle A S Lemke
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA.,Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Stephanie M Olson
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA.,Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Kaitlin Morse
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Steven D Karlen
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA.,Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Alan Higbee
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA.,Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA
| | - Emily T Beebe
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - John Ralph
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA.,Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Joshua J Coon
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA.,Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA.,Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Brian G Fox
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA.,Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Timothy J Donohue
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA .,Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
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19
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Reduction of Protein Bound Methionine Sulfoxide by a Periplasmic Dimethyl Sulfoxide Reductase. Antioxidants (Basel) 2020; 9:antiox9070616. [PMID: 32674377 PMCID: PMC7402097 DOI: 10.3390/antiox9070616] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 01/16/2023] Open
Abstract
In proteins, methionine (Met) can be oxidized into Met sulfoxide (MetO). The ubiquitous methionine sulfoxide reductases (Msr) A and B are thiol-oxidoreductases reducing MetO. Reversible Met oxidation has a wide range of consequences, from protection against oxidative stress to fine-tuned regulation of protein functions. Bacteria distinguish themselves by the production of molybdenum-containing enzymes reducing MetO, such as the periplasmic MsrP which protects proteins during acute oxidative stress. The versatile dimethyl sulfoxide (DMSO) reductases were shown to reduce the free amino acid MetO, but their ability to reduce MetO within proteins was never evaluated. Here, using model oxidized proteins and peptides, enzymatic and mass spectrometry approaches, we showed that the Rhodobacter sphaeroides periplasmic DorA-type DMSO reductase reduces protein bound MetO as efficiently as the free amino acid L-MetO and with catalytic values in the range of those described for the canonical Msrs. The identification of this fourth type of enzyme able to reduce MetO in proteins, conserved across proteobacteria and actinobacteria, suggests that organisms employ enzymatic systems yet undiscovered to regulate protein oxidation states.
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20
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Oxidative Stress and Antioxidant Responses of Phormidium ambiguum and Microcystis aeruginosa Under Diurnally Varying Light Conditions. Microorganisms 2020; 8:microorganisms8060890. [PMID: 32545576 PMCID: PMC7357134 DOI: 10.3390/microorganisms8060890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 12/22/2022] Open
Abstract
Two harmful cyanobacteria species (Phormidium ambiguum and Microcystis aeruginosa) were exposed to diurnal light-intensity variation to investigate their favorable and stressed phases during a single day. The photosynthetically active radiation (PAR) started at 0 µmol·m−2·s−1 (06:00 h), increased by ~25 µmol·m−2·s−1 or ~50 µmol·m−2·s−1 every 30 min, peaking at 300 µmol·m−2·s−1 or 600 µmol·m−2·s−1 (12:00 h), and then decreased to 0 µmol·m−2·s−1 (by 18:00 h). The H2O2 and antioxidant activities were paralleled to light intensity. Higher H2O2 and antioxidant levels (guaiacol peroxidase, catalase (CAT), and superoxidase dismutase) were observed at 600 µmol·m−2·s−1 rather than at 300 µmol·m−2·s−1. Changes in antioxidant levels under each light condition differed between the species. Significant correlations were observed between antioxidant activities and H2O2 contents for both species, except for the CAT activity of P. ambiguum at 300 µmol·m−2·s−1. Under each of the conditions, both species responded proportionately to oxidative stress. Even under maximum light intensities (300 µmol·m−2·s−1 or 600 µmol·m−2·s−1 PAR intensity), neither species was stressed. Studies using extended exposure durations are warranted to better understand the growth performance and long-term physiological responses of both species.
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21
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Adaptation to Photooxidative Stress: Common and Special Strategies of the Alphaproteobacteria Rhodobacter sphaeroides and Rhodobacter capsulatus. Microorganisms 2020; 8:microorganisms8020283. [PMID: 32093084 PMCID: PMC7074977 DOI: 10.3390/microorganisms8020283] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/20/2022] Open
Abstract
Photosynthetic bacteria have to deal with the risk of photooxidative stress that occurs in presence of light and oxygen due to the photosensitizing activity of (bacterio-) chlorophylls. Facultative phototrophs of the genus Rhodobacter adapt the formation of photosynthetic complexes to oxygen and light conditions, but cannot completely avoid this stress if environmental conditions suddenly change. R. capsulatus has a stronger pigmentation and faster switches to phototrophic growth than R. sphaeroides. However, its photooxidative stress response has not been investigated. Here, we compare both species by transcriptomics and proteomics, revealing that proteins involved in oxidation-reduction processes, DNA, and protein damage repair play pivotal roles. These functions are likely universal to many phototrophs. Furthermore, the alternative sigma factors RpoE and RpoHII are induced in both species, even though the genetic localization of the rpoE gene, the RpoE protein itself, and probably its regulon, are different. Despite sharing the same habitats, our findings also suggest individual strategies. The crtIB-tspO operon, encoding proteins for biosynthesis of carotenoid precursors and a regulator of photosynthesis, and cbiX, encoding a putative ferrochelatase, are induced in R. capsulatus. This specific response might support adaptation by maintaining high carotenoid-to-bacteriochlorophyll ratios and preventing the accumulation of porphyrin-derived photosensitizers.
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22
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Nie X, Remes B, Klug G. Multiple Sense and Antisense Promoters Contribute to the Regulated Expression of the isc-suf Operon for Iron-Sulfur Cluster Assembly in Rhodobacter. Microorganisms 2019; 7:microorganisms7120671. [PMID: 31835540 PMCID: PMC6956336 DOI: 10.3390/microorganisms7120671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 11/16/2022] Open
Abstract
A multitude of biological functions relies on iron-sulfur clusters. The formation of photosynthetic complexes goes along with an additional demand for iron-sulfur clusters for bacteriochlorophyll synthesis and photosynthetic electron transport. However, photooxidative stress leads to the destruction of iron-sulfur clusters, and the released iron promotes the formation of further reactive oxygen species. A balanced regulation of iron-sulfur cluster synthesis is required to guarantee the supply of this cofactor, on the one hand, but also to limit stress, on the other hand. The phototrophic alpha-proteobacterium Rhodobacter sphaeroides harbors a large operon for iron-sulfur cluster assembly comprising the iscRS and suf genes. IscR (iron-sulfur cluster regulator) is an iron-dependent regulator of isc-suf genes and other genes with a role in iron metabolism. We applied reporter gene fusions to identify promoters of the isc-suf operon and studied their activity alone or in combination under different conditions. Gel-retardation assays showed the binding of regulatory proteins to individual promoters. Our results demonstrated that several promoters in a sense and antisense direction influenced isc-suf expression and the binding of the IscR, Irr, and OxyR regulatory proteins to individual promoters. These findings demonstrated a complex regulatory network of several promoters and regulatory proteins that helped to adjust iron-sulfur cluster assembly to changing conditions in Rhodobacter sphaeroides.
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Abstract
This year marks the 50th anniversary of the discovery of σ70 as a protein factor that was needed for bacterial RNA polymerase to accurately transcribe a promoter in vitro. It was 25 years later that the Group IV alternative σs were described as a distinct family of proteins related to σ70 . In the intervening time, there has been an ever-growing list of Group IV σs, numbers of genes they transcribe, insight into the diverse suite of processes they control, and appreciation for their impact on bacterial lifestyles. This work summarizes knowledge of the Rhodobacter sphaeroides σE -ChrR pair, a member of the ECF11 subfamily of Group IV alternative σs, in protecting cells from the reactive oxygen species, singlet oxygen. It describes lessons learned from analyzing ChrR, a zinc-dependent anti-σ factor, that are generally applicable to Group IV σs and relevant to the response to single oxygen. This MicroReview also illustrates insights into stress responses in this and other bacteria that have been acquired by analyzing or modeling the activity of the σE -ChrR across the bacterial phylogeny.
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Affiliation(s)
- Timothy J. Donohue
- Bacteriology Department, Great Lakes Bioenergy Research CenterWisconsin Energy Institute, University of Wisconsin‐MadisonMadisonWI53726USA
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Park JH, Lee JH, Roe JH. SigR, a hub of multilayered regulation of redox and antibiotic stress responses. Mol Microbiol 2019; 112:420-431. [PMID: 31269533 DOI: 10.1111/mmi.14341] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2019] [Indexed: 02/01/2023]
Abstract
Signal-specific activation of alternative sigma factors redirects RNA polymerase to induce transcription of distinct sets of genes conferring protection against the damage the signal and the related stresses incur. In Streptomyces coelicolor, σR (SigR), a member of ECF12 subfamily of Group IV sigma factors, responds to thiol-perturbing signals such as oxidants and electrophiles, as well as to translation-blocking antibiotics. Oxidants and electrophiles interact with and inactivate the zinc-containing anti-sigma factor, RsrA, via disulfide bond formation or alkylation of reactive cysteines, subsequently releasing σR for target gene induction. Translation-blocking antibiotics induce the synthesis of σR , via the WhiB-like transcription factor, WblC/WhiB7. Signal transduction via RsrA produces a dramatic transient response that involves positive feedback to produce more SigR as an unstable isoform σ R ' and negative feedbacks to degrade σ R ' , and reduce oxidized RsrA that subsequently sequester σR and σ R ' . Antibiotic stress brings about a prolonged response by increasing stable σR levels. The third negative feedback, which occurs via IF3, lowers the translation efficiency of the sigRp1 transcript that utilizes a non-canonical start codon. σR is a global regulator that directly activates > 100 transcription units in S. coelicolor, including genes for thiol homeostasis, protein quality control, sulfur metabolism, ribosome modulation and DNA repair. Close homologues in Actinobacteria, such as σH in Mycobacteria and Corynebacteria, show high conservation of the signal transduction pathways and target genes, thus reflecting the robustness of this type of regulation in response to redox and antibiotic stresses.
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Affiliation(s)
- Joo-Hong Park
- School of Biological Sciences, and Institute of Microbiology, College of Natural Sciences, Seoul National University, Seoul, Korea
| | - Ju-Hyung Lee
- School of Biological Sciences, and Institute of Microbiology, College of Natural Sciences, Seoul National University, Seoul, Korea
| | - Jung-Hye Roe
- School of Biological Sciences, and Institute of Microbiology, College of Natural Sciences, Seoul National University, Seoul, Korea
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Lonetto MA, Donohue TJ, Gross CA, Buttner MJ. Discovery of the extracytoplasmic function σ factors. Mol Microbiol 2019; 112:348-355. [PMID: 31115926 DOI: 10.1111/mmi.14307] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2019] [Indexed: 12/14/2022]
Abstract
This special issue of Molecular Microbiology marks the 25th anniversary of the discovery of the extracytoplasmic function (ECF) σ factors, proteins that subsequently emerged as the largest group of alternative σ factors and one of the three major pillars of signal transduction in bacteria, alongside one- and two-component systems. A single bacterial genome can encode > 100 ECF σ factors, and combined with their cognate anti-σ factors, they represent a modular design that primarily functions in transmembrane signal transduction. Here, we first describe the immediate events that led to the 1994 publication in the Proceeding of the National Academy of Sciences USA, and then set them in the broader context of key events in the history of σ biology research.
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Affiliation(s)
- Michael A Lonetto
- Department of Informatics, Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Timothy J Donohue
- Department of Bacteriology, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53706, USA
| | - Carol A Gross
- Department of Microbiology and Immunology and Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Zhao Z, Peng T, Oh JI, Glaeser J, Weber L, Li Q, Klug G. A response regulator of the OmpR family is part of the regulatory network controlling the oxidative stress response of Rhodobacter sphaeroides. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:118-128. [PMID: 30451391 DOI: 10.1111/1758-2229.12718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/12/2018] [Indexed: 06/09/2023]
Abstract
As a free-living bacterium Rhodobacter sphaeroides needs to respond to many environmental stresses. Oxidative stress, membrane stress or heat stress induce the ompR-1 gene encoding a protein of the OmpR family. Overexpression of OmpR-1 results in increased resistance to organic peroxides and diamide. Our data demonstrate that OmpR-1 positively affects expression of several sRNAs with an established role in R. sphaeroides stress defences and negatively affects the promoter of the rpoHI gene. The RpoHI sigma factor has a main role in the activation of many stress responses. Thus OmpR-1 has a balancing effect on the activation of the RpoHI regulon. We present a model with OmpR-1 as part of a regulatory network controlling stress defences in R. sphaeroides.
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Affiliation(s)
- Zhiping Zhao
- Institut für Mikrobiologie und Molekularbiologie, Interdiziplinäres Forschungszentrum, Justus-Liebig-Universität Giessen, Giessen, Germany
- Department of Pharmaceutical Engineering, Sichuan University of Science and Engineering, Zigong, China
| | | | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, Busan, South Korea
| | - Jens Glaeser
- Institut für Mikrobiologie und Molekularbiologie, Interdiziplinäres Forschungszentrum, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Lennart Weber
- Institut für Mikrobiologie und Molekularbiologie, Interdiziplinäres Forschungszentrum, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Qingfeng Li
- Institut für Mikrobiologie und Molekularbiologie, Interdiziplinäres Forschungszentrum, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Gabriele Klug
- Institut für Mikrobiologie und Molekularbiologie, Interdiziplinäres Forschungszentrum, Justus-Liebig-Universität Giessen, Giessen, Germany
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Adaptations and evolution of a heritable leaf nodule symbiosis between Dioscorea sansibarensis and Orrella dioscoreae. ISME JOURNAL 2019; 13:1831-1844. [PMID: 30877285 DOI: 10.1038/s41396-019-0398-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022]
Abstract
Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis between a wild yam species from Madagascar, Dioscorea sansibarensis and bacteria of the species Orrella dioscoreae. Using whole-genome sequencing of plastids and bacteria from wild-collected samples, we show phylogenetic patterns consistent with a dominant vertical mode of transmission of the symbionts. Unique so far among leaf nodule symbioses, the bacteria can be cultured and are amenable to comparative transcriptomics, revealing a potential role in complementing the host's arsenal of secondary metabolites. We propose a recent establishment of a vertical mode of transmission in this symbiosis which, together with a large effective population size explains the cultivability and apparent lack of genome reductive evolution in O. dioscoreae. We leverage these unique features to reveal pathways and functions under positive selection in these specialized endophytes, highlighting the candidate mechanisms enabling a permanent association in the phyllosphere.
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Förstner KU, Reuscher CM, Haberzettl K, Weber L, Klug G. RNase E cleavage shapes the transcriptome ofRhodobacter sphaeroidesand strongly impacts phototrophic growth. Life Sci Alliance 2018; 1:e201800080. [PMID: 30456366 PMCID: PMC6238624 DOI: 10.26508/lsa.201800080] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/13/2018] [Accepted: 07/13/2018] [Indexed: 11/24/2022] Open
Abstract
This study identifies the cleavage sites of the endoribonuclease RNase E in the Rhodobacter sphaeroides transcriptome and demonstrates its effect on oxidative stress resistance and phototrophic growth. Bacteria adapt to changing environmental conditions by rapid changes in their transcriptome. This is achieved not only by adjusting rates of transcription but also by processing and degradation of RNAs. We applied TIER-Seq (transiently inactivating an endoribonuclease followed by RNA-Seq) for the transcriptome-wide identification of RNase E cleavage sites and of 5′ RNA ends, which are enriched when RNase E activity is reduced in Rhodobacter sphaeroides. These results reveal the importance of RNase E for the maturation and turnover of mRNAs, rRNAs, and sRNAs in this guanine-cytosine-rich α-proteobacterium, some of the latter have well-described functions in the oxidative stress response. In agreement with this, a role of RNase E in the oxidative stress response is demonstrated. A remarkably strong phenotype of a mutant with reduced RNase E activity was observed regarding the formation of photosynthetic complexes and phototrophic growth, whereas there was no effect on chemotrophic growth.
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Affiliation(s)
- Konrad U Förstner
- German National Library of Medicine—Information Center for Life Sciences, Cologne, Germany
- Technical University of Cologne, Faculty for Information and Communication Sciences, Cologne, Germany
- Core Unit Systems Medicine, Institutes of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
- Correspondence:
| | - Carina M Reuscher
- Institut für Mikrobiologie und Molekularbiologie, Interdisciplinary Research Center for Biosystems, Universität Giessen, Giessen, Germany
| | - Kerstin Haberzettl
- Institut für Mikrobiologie und Molekularbiologie, Interdisciplinary Research Center for Biosystems, Universität Giessen, Giessen, Germany
| | - Lennart Weber
- Institut für Mikrobiologie und Molekularbiologie, Interdisciplinary Research Center for Biosystems, Universität Giessen, Giessen, Germany
| | - Gabriele Klug
- Institut für Mikrobiologie und Molekularbiologie, Interdisciplinary Research Center for Biosystems, Universität Giessen, Giessen, Germany
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Bacellar IOL, Oliveira MC, Dantas LS, Costa EB, Junqueira HC, Martins WK, Durantini AM, Cosa G, Di Mascio P, Wainwright M, Miotto R, Cordeiro RM, Miyamoto S, Baptista MS. Photosensitized Membrane Permeabilization Requires Contact-Dependent Reactions between Photosensitizer and Lipids. J Am Chem Soc 2018; 140:9606-9615. [DOI: 10.1021/jacs.8b05014] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Isabel O. L. Bacellar
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Prof. Lineu Prestes 748, São Paulo, SP, Brazil, 05508-000
- Department of Chemistry and Center for Self-Assembled Chemical Structures CSACS/CRMAA, McGill University, 801 Sherbrook Street West, Montreal, QC, Canada, H3A 0B8
| | - Maria Cecilia Oliveira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, Santo André, SP, Brazil, 09210-580
| | - Lucas S. Dantas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Prof. Lineu Prestes 748, São Paulo, SP, Brazil, 05508-000
| | - Elierge B. Costa
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, Santo André, SP, Brazil, 09210-580
| | - Helena C. Junqueira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Prof. Lineu Prestes 748, São Paulo, SP, Brazil, 05508-000
| | - Waleska K. Martins
- Universidade Anhanguera de São Paulo, Avenida Raimundo Pereira de Magalhães, 3305, São Paulo, SP, Brazil, 05145-200
| | - Andrés M. Durantini
- Department of Chemistry and Center for Self-Assembled Chemical Structures CSACS/CRMAA, McGill University, 801 Sherbrook Street West, Montreal, QC, Canada, H3A 0B8
| | - Gonzalo Cosa
- Department of Chemistry and Center for Self-Assembled Chemical Structures CSACS/CRMAA, McGill University, 801 Sherbrook Street West, Montreal, QC, Canada, H3A 0B8
| | - Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Prof. Lineu Prestes 748, São Paulo, SP, Brazil, 05508-000
| | - Mark Wainwright
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom, L3 3AF
| | - Ronei Miotto
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, Santo André, SP, Brazil, 09210-580
| | - Rodrigo M. Cordeiro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, Santo André, SP, Brazil, 09210-580
| | - Sayuri Miyamoto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Prof. Lineu Prestes 748, São Paulo, SP, Brazil, 05508-000
| | - Mauricio S. Baptista
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Prof. Lineu Prestes 748, São Paulo, SP, Brazil, 05508-000
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The PhyR homolog RSP_1274 of Rhodobacter sphaeroides is involved in defense of membrane stress and has a moderate effect on RpoE (RSP_1092) activity. BMC Microbiol 2018; 18:18. [PMID: 29486719 PMCID: PMC5830050 DOI: 10.1186/s12866-018-1161-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/20/2018] [Indexed: 11/10/2022] Open
Abstract
Background A major role of the PhyR-NepR-σ(EcfG) cascade in the general stress response was demonstrated for some bacterial species and considered as conserved in Alphaproteobacteria. The σ(EcfG) factor activates its target genes in response to diverse stresses and NepR represents its anti-sigma factor. PhyR comprises a response regulator domain and a sigma factor domain and acts as anti-sigma factor antagonist. The facultative phototrophic alphaproteobacterium Rhodobacter sphaeroides harbours a PhyR homolog in the same genomic context as found in other members of this class. Results Our study reveals increased expression of the phyR gene in response to superoxide, singlet oxygen, and diamide and also an effect of PhyR on rpoE expression. RpoE has a central role in mounting the response to singlet oxygen in R. sphaeroides. Despite these findings a mutant lacking PhyR was not significantly impeded in resistance to oxidative stress, heat stress or osmotic stress. However a role of PhyR in membrane stress is demonstrated. Conclusion These results support the view that the effect of the PhyR-NepR-σ(EcfG) cascade on diverse stress responses varies among members of the Alphaproteobacteria. In the facultative phototroph Rhodobacter sphaeroides PhyR plays no major role in the general stress or the oxidative stress response but rather has a more specialized role in defense of membrane stress. Electronic supplementary material The online version of this article (10.1186/s12866-018-1161-4) contains supplementary material, which is available to authorized users.
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Muñoz P, Munné-Bosch S. Photo-Oxidative Stress during Leaf, Flower and Fruit Development. PLANT PHYSIOLOGY 2018; 176:1004-1014. [PMID: 29051197 PMCID: PMC5813531 DOI: 10.1104/pp.17.01127] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/18/2017] [Indexed: 05/07/2023]
Abstract
Photooxidative stress plays a crucial role in organ growth and development, with some similarities but also important differences in the development of leaves, flowers, and fruits.
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Affiliation(s)
- Paula Muñoz
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain 08028
| | - Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain 08028
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An RpoHI-Dependent Response Promotes Outgrowth after Extended Stationary Phase in the Alphaproteobacterium Rhodobacter sphaeroides. J Bacteriol 2017; 199:JB.00249-17. [PMID: 28507242 DOI: 10.1128/jb.00249-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/05/2017] [Indexed: 12/31/2022] Open
Abstract
Under unfavorable growth conditions, bacteria enter stationary phase and can maintain cell viability over prolonged periods with no increase in cell number. To obtain insights into the regulatory mechanisms that allow bacteria to resume growth when conditions become favorable again (outgrowth), we performed global transcriptome analyses at different stages of growth for the alphaproteobacterium Rhodobacter sphaeroides The majority of genes were not differentially expressed across growth phases. After a short stationary phase (about 20 h after growth starts to slow down), only 7% of the genes showed altered expression (fold change of >1.6 or less than -1.6, corresponding to a log2 fold change of >0.65 or less than -0.65, respectively) compared to expression at exponential phase. Outgrowth induced a distinct response in gene expression which was strongly influenced by the length of the preceding stationary phase. After a long stationary phase (about 64 h after growth starts to slow down), a much larger number of genes (15.1%) was induced in outgrowth than after a short stationary phase (1.7%). Many of those genes are known members of the RpoHI/RpoHII regulons and have established functions in stress responses. A main effect of RpoHI on the transcriptome in outgrowth after a long stationary phase was confirmed. Growth experiments with mutant strains further support an important function in outgrowth after prolonged stationary phase for the RpoHI and RpoHII sigma factors.IMPORTANCE In natural environments, the growth of bacteria is limited mostly by lack of nutrients or other unfavorable conditions. It is important for bacterial populations to efficiently resume growth after being in stationary phase, which may last for long periods. Most previous studies on growth-phase-dependent gene expression did not address outgrowth after stationary phase. This study on growth-phase-dependent gene regulation in a model alphaproteobacterium reveals, for the first time, that the length of the stationary phase strongly impacts the transcriptome during outgrowth. The alternative sigma factors RpoHI and RpoHII, which are important regulators of stress responses in alphaproteobacteria, play a major role during outgrowth following prolonged stationary phase. These findings provide the first insight into the regulatory mechanisms enabling efficient outgrowth.
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Carotenoid production and phenotypic variation in Azospirillum brasilense. Res Microbiol 2017; 168:493-501. [DOI: 10.1016/j.resmic.2017.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/17/2017] [Accepted: 02/21/2017] [Indexed: 11/22/2022]
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Sineva E, Savkina M, Ades SE. Themes and variations in gene regulation by extracytoplasmic function (ECF) sigma factors. Curr Opin Microbiol 2017; 36:128-137. [PMID: 28575802 DOI: 10.1016/j.mib.2017.05.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/15/2017] [Accepted: 05/13/2017] [Indexed: 01/08/2023]
Abstract
The ECF sigma family was identified 23 years ago as a distinct group of σ70-like factors. ECF sigma factors have since emerged as a major form of bacterial signal transduction that can be grouped into over 50 phylogenetically distinct subfamilies. Advances in our understanding of these sigma factors and the signaling pathways governing their activity have elucidated conserved features as well as aspects that have evolved over time. All ECF sigma factors are predicted to share a common streamlined domain structure and mode of promoter interaction. The activity of most ECF sigma factors is controlled by an anti-sigma factor. The nature of the anti-sigma factor and the activating signaling pathways appear to be conserved within ECF families, while considerable diversity exists between different families.
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Affiliation(s)
- Elena Sineva
- Department of Biochemistry and Molecular Biology, 408 Althouse Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
| | - Maria Savkina
- Department of Biochemistry and Molecular Biology, 408 Althouse Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah E Ades
- Department of Biochemistry and Molecular Biology, 408 Althouse Laboratory, The Pennsylvania State University, University Park, PA 16802, USA.
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Structural insights into the regulation of Bacillus subtilis SigW activity by anti-sigma RsiW. PLoS One 2017; 12:e0174284. [PMID: 28319136 PMCID: PMC5358783 DOI: 10.1371/journal.pone.0174284] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/06/2017] [Indexed: 11/19/2022] Open
Abstract
Bacillus subtilis SigW is localized to the cell membrane and is inactivated by the tight interaction with anti-sigma RsiW under normal growth conditions. Whereas SigW is discharged from RsiW binding and thus initiates the transcription of its regulon under diverse stress conditions such as antibiotics and alkaline shock. The release and activation of SigW in response to extracytoplasmic signals is induced by the regulated intramembrane proteolysis of RsiW. As a ZAS (Zinc-containing anti-sigma) family protein, RsiW has a CHCC zinc binding motif, which implies that its anti-sigma activity may be regulated by the state of zinc coordination in addition to the proteolytic cleavage of RsiW. To understand the regulation mode of SigW activity by RsiW, we determined the crystal structures of SigW in complex with the cytoplasmic domain of RsiW, and compared the conformation of the CHCC motif in the reduced/zinc binding and the oxidized states. The structures revealed that RsiW inhibits the promoter binding of SigW by interacting with the surface groove of SigW. The interaction between SigW and RsiW is not disrupted by the oxidation of the CHCC motif in RsiW, suggesting that SigW activity might not be regulated by the zinc coordination states of the CHCC motif.
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Tardu M, Bulut S, Kavakli IH. MerR and ChrR mediate blue light induced photo-oxidative stress response at the transcriptional level in Vibrio cholerae. Sci Rep 2017; 7:40817. [PMID: 28098242 PMCID: PMC5241685 DOI: 10.1038/srep40817] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/09/2016] [Indexed: 12/14/2022] Open
Abstract
Blue light (BL) is a major environmental factor that affects the physiology, behavior, and infectivity of bacteria as it contributes to the generation of reactive oxygen species (ROS) while increasing photo-oxidative stress in cells. However, precise photo-oxidative response mechanism in non-phototrophic bacteria is yet to be elucidated. In this study, we investigated the effect of BL in Vibrio cholerae by using genetics and transcriptome profiling. Genome-wide analysis revealed that transcription of 6.3% of V. cholerae genes were regulated by BL. We further showed that BL enhances ROS production, which is generated through the oxidative phosphorylation. To understand signaling mechanisms, we generated several knockouts and analyzed their transcriptome under BL exposure. Studies with a double-knockout confirm an anti-sigma factor (ChrR) and putative metalloregulatory-like protein (MerR) are responsible for the genome-wide regulation to BL response in V. cholerae. Collectively, these results demonstrate that MerR-like proteins, in addition to ChrR, are required for V. cholerae to mount an appropriate response against photo-oxidative stress induced by BL. Outside its natural host, V. cholerae can survive for extended periods in natural aquatic environments. Therefore, the regulation of light response for V. cholerae may be a critical cellular process for its survival in these environments.
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Affiliation(s)
- Mehmet Tardu
- Computational Science and Engineering, Koc University, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey
| | - Selma Bulut
- Chemical and Biological Engineering, Koc University, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey
| | - Ibrahim Halil Kavakli
- Computational Science and Engineering, Koc University, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey.,Chemical and Biological Engineering, Koc University, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey.,Molecular Biology and Genetics, Koc University, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey
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Chakraborty J, Nath I, Verpoort F. Snapshots of encapsulated porphyrins and heme enzymes in metal-organic materials: A prevailing paradigm of heme mimicry. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Carotenoid Biosynthetic Pathways Are Regulated by a Network of Multiple Cascades of Alternative Sigma Factors in Azospirillum brasilense Sp7. J Bacteriol 2016; 198:2955-2964. [PMID: 27551017 DOI: 10.1128/jb.00460-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 07/30/2016] [Indexed: 11/20/2022] Open
Abstract
Carotenoids constitute an important component of the defense system against photooxidative stress in bacteria. In Azospirillum brasilense Sp7, a nonphotosynthetic rhizobacterium, carotenoid synthesis is controlled by a pair of extracytoplasmic function sigma factors (RpoEs) and their cognate zinc-binding anti-sigma factors (ChrRs). Its genome harbors two copies of the gene encoding geranylgeranyl pyrophosphate synthase (CrtE), the first critical step in the carotenoid biosynthetic pathway in bacteria. Inactivation of each of two crtE paralogs found in A. brasilense caused reduction in carotenoid content, suggesting their involvement in carotenoid synthesis. However, the effect of crtE1 deletion was more pronounced than that of crtE2 deletion. Out of the five paralogs of rpoH in A. brasilense, overexpression of rpoH1 and rpoH2 enhanced carotenoid synthesis. Promoters of crtE2 and rpoH2 were found to be dependent on RpoH2 and RpoE1, respectively. Using a two-plasmid system in Escherichia coli, we have shown that the crtE2 gene of A. brasilense Sp7 is regulated by two cascades of sigma factors: one consisting of RpoE1and RpoH2 and the other consisting of RpoE2 and RpoH1. In addition, expression of crtE1 was upregulated indirectly by RpoE1 and RpoE2. This study shows, for the first time in any carotenoid-producing bacterium, that the regulation of carotenoid biosynthetic pathway involves a network of multiple cascades of alternative sigma factors. IMPORTANCE Carotenoids play a very important role in coping with photooxidative stress in prokaryotes and eukaryotes. Although extracytoplasmic function (ECF) sigma factors are known to directly regulate the expression of carotenoid biosynthetic genes in bacteria, regulation of carotenoid biosynthesis by one or multiple cascades of sigma factors had not been reported. This study provides the first evidence of the involvement of multiple cascades of sigma factors in the regulation of carotenoid synthesis in any bacterium by showing the regulation of a gene encoding geranylgeranyl pyrophosphate synthase (crtE2) by RpoE1→RpoH2→CrtE2 and RpoE2→RpoH1→CrtE2 cascades in A. brasilense It also provides an insight into existence of an additional cascade or cascades regulating expression of another paralog of crtE.
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The anti-sigma factor RsrA responds to oxidative stress by reburying its hydrophobic core. Nat Commun 2016; 7:12194. [PMID: 27432510 PMCID: PMC4960319 DOI: 10.1038/ncomms12194] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 06/08/2016] [Indexed: 12/22/2022] Open
Abstract
Redox-regulated effector systems that counteract oxidative stress are essential for all forms of life. Here we uncover a new paradigm for sensing oxidative stress centred on the hydrophobic core of a sensor protein. RsrA is an archetypal zinc-binding anti-sigma factor that responds to disulfide stress in the cytoplasm of Actinobacteria. We show that RsrA utilizes its hydrophobic core to bind the sigma factor σR preventing its association with RNA polymerase, and that zinc plays a central role in maintaining this high-affinity complex. Oxidation of RsrA is limited by the rate of zinc release, which weakens the RsrA–σR complex by accelerating its dissociation. The subsequent trigger disulfide, formed between specific combinations of RsrA's three zinc-binding cysteines, precipitates structural collapse to a compact state where all σR-binding residues are sequestered back into its hydrophobic core, releasing σR to activate transcription of anti-oxidant genes. Counteracting oxidative stress is essential in all organisms. Here, the authors outline a mechanism used by actinomycete bacteria in which oxidation of zinc-binding RsrA blocks its interaction with σR by sequestering hydrophobic residues used to bind σR within its own core.
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Peng T, Berghoff BA, Oh JI, Weber L, Schirmer J, Schwarz J, Glaeser J, Klug G. Regulation of a polyamine transporter by the conserved 3' UTR-derived sRNA SorX confers resistance to singlet oxygen and organic hydroperoxides in Rhodobacter sphaeroides. RNA Biol 2016; 13:988-999. [PMID: 27420112 DOI: 10.1080/15476286.2016.1212152] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Singlet oxygen is generated by bacteriochlorophylls when light and oxygen are simultaneously present in Rhodobacter sphaeroides. Singlet oxygen triggers a specific response that is partly regulated by the alternative sigma factor RpoHI/HII. The sRNA RSs2461 has previously been identified as an RpoHI/HII-dependent sRNA and is derived from the 3' UTR of the mRNA for an OmpR-type transcriptional regulator. Similar to the RpoHI/HII-dependent CcsR and SorY sRNAs, RSs2461 affects the resistance of R. sphaeroides against singlet oxygen and was therefore renamed here SorX. Furthermore, SorX has a strong impact on resistance against organic hydroperoxides that usually occur as secondary damages downstream of singlet oxygen. The 75-nt SorX 3' fragment, which is generated by RNase E cleavage and highly conserved among related species, represents the functional entity. A target search identified potA mRNA, which encodes a subunit of a polyamine transporter, as a direct SorX target and stress resistance via SorX could be linked to potA. The PotABCD transporter is an uptake system for spermidine in E. coli. While spermidine is generally described as beneficial during oxidative stress, we observed significantly increased sensitivity of R. sphaeroides to organic hydroperoxides in the presence of spermidine. We therefore propose that the diminished import of spermidine, due to down-regulation of potA by SorX, counteracts oxidative stress. Together with results from other studies this underlines the importance of regulated transport to bacterial stress defense.
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Affiliation(s)
- Tao Peng
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Bork A Berghoff
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Jeong-Il Oh
- b Department of Microbiology , Pusan National University , Busan , Korea
| | - Lennart Weber
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Jasmin Schirmer
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Johannes Schwarz
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Jens Glaeser
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Gabriele Klug
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
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López-Leal G, Cevallos MA, Castillo-Ramírez S. Evolution of a Sigma Factor: An All-In-One of Gene Duplication, Horizontal Gene Transfer, Purifying Selection, and Promoter Differentiation. Front Microbiol 2016; 7:581. [PMID: 27199915 PMCID: PMC4843759 DOI: 10.3389/fmicb.2016.00581] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/08/2016] [Indexed: 01/11/2023] Open
Abstract
Sigma factors are an essential part of bacterial gene regulation and have been extensively studied as far as their molecular mechanisms and protein structure are concerned. However, their molecular evolution, especially for the alternative sigma factors, is poorly understood. Here, we analyze the evolutionary forces that have shaped the rpoH sigma factors within the alphaproteobacteria. We found that an ancient duplication gave rise to two major groups of rpoH sigma factors and that after this event horizontal gene transfer (HGT) occurred in rpoH1 group. We also noted that purifying selection has differentially affected distinct parts of the gene; singularly, the gene segment that encodes the region 4.2, which interacts with the −35 motif of the RpoH-dependent genes, has been under relaxed purifying selection. Furthermore, these two major groups are clearly differentiated from one another regarding their promoter selectivity, as rpoH1 is under the transcriptional control of σ70 and σ32, whereas rpoH2 is under the transcriptional control of σ24. Our results suggest a scenario in which HGT, gene loss, variable purifying selection and clear promoter specialization occurred after the ancestral duplication event. More generally, our study offers insights into the molecular evolution of alternative sigma factors and highlights the importance of analyzing not only the coding regions but also the promoter regions.
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Affiliation(s)
- Gamaliel López-Leal
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Miguel A Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
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Adnan F, Weber L, Klug G. The sRNA SorY confers resistance during photooxidative stress by affecting a metabolite transporter in Rhodobacter sphaeroides. RNA Biol 2016; 12:569-77. [PMID: 25833751 PMCID: PMC4615379 DOI: 10.1080/15476286.2015.1031948] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Exposure to oxygen and light generates photooxidative stress by the bacteriochlorophyll a mediated formation of singlet oxygen (1O2) in the facultative photosynthetic bacterium Rhodobacter sphaeroides. We have identified SorY as an sRNA, which is induced under several stress conditions and confers increased resistance against 1O2. SorY by direct interaction affects the takP mRNA, encoding a TRAP-T transporter. We present a model in which SorY reduces the metabolite flux into the tricarboxylic acid cycle (TCA cycle) by reducing malate import through TakP. It was previously shown that oxidative stress in bacteria leads to switch from glycolysis to the pentose phosphate pathway and to reduced activity of the TCA cycle. As a consequence the production of the prooxidant NADH is reduced and production of the protective NADPH is enhanced. In R. sphaeroides enzymes for glycolysis, pentose phosphate pathway, Entner–Doudoroff pathway and gluconeogenesis are induced in response to 1O2 by the alternative sigma factor RpoHII. The same is true for the sRNA SorY. By limiting malate import SorY thus contributes to the balance of the metabolic fluxes under photooxidative stress conditions. This assigns a so far unknown function to an sRNA in oxidative stress response.
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Affiliation(s)
- Fazal Adnan
- a Institute of Microbiology and Molecular Biology ; IFZ ; Giessen University ; Giessen , Germany
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Mattila H, Khorobrykh S, Havurinne V, Tyystjärvi E. Reactive oxygen species: Reactions and detection from photosynthetic tissues. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 152:176-214. [PMID: 26498710 DOI: 10.1016/j.jphotobiol.2015.10.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 12/22/2022]
Abstract
Reactive oxygen species (ROS) have long been recognized as compounds with dual roles. They cause cellular damage by reacting with biomolecules but they also function as agents of cellular signaling. Several different oxygen-containing compounds are classified as ROS because they react, at least with certain partners, more rapidly than ground-state molecular oxygen or because they are known to have biological effects. The present review describes the typical reactions of the most important ROS. The reactions are the basis for both the detection methods and for prediction of reactions between ROS and biomolecules. Chemical and physical methods used for detection, visualization and quantification of ROS from plants, algae and cyanobacteria will be reviewed. The main focus will be on photosynthetic tissues, and limitations of the methods will be discussed.
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Affiliation(s)
- Heta Mattila
- Department of Biochemistry/Molecular Plant Biology, University of Turku, 20014 Turku, Finland
| | - Sergey Khorobrykh
- Department of Biochemistry/Molecular Plant Biology, University of Turku, 20014 Turku, Finland
| | - Vesa Havurinne
- Department of Biochemistry/Molecular Plant Biology, University of Turku, 20014 Turku, Finland
| | - Esa Tyystjärvi
- Department of Biochemistry/Molecular Plant Biology, University of Turku, 20014 Turku, Finland.
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Erickson E, Wakao S, Niyogi KK. Light stress and photoprotection in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:449-465. [PMID: 25758978 DOI: 10.1111/tpj.12825] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 03/05/2015] [Accepted: 03/06/2015] [Indexed: 05/18/2023]
Abstract
Plants and algae require light for photosynthesis, but absorption of too much light can lead to photo-oxidative damage to the photosynthetic apparatus and sustained decreases in the efficiency and rate of photosynthesis (photoinhibition). Light stress can adversely affect growth and viability, necessitating that photosynthetic organisms acclimate to different environmental conditions in order to alleviate the detrimental effects of excess light. The model unicellular green alga, Chlamydomonas reinhardtii, employs diverse strategies of regulation and photoprotection to avoid, minimize, and repair photo-oxidative damage in stressful light conditions, allowing for acclimation to different and changing environments.
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Affiliation(s)
- Erika Erickson
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Setsuko Wakao
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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Soora M, Tomasch J, Wang H, Michael V, Petersen J, Engelen B, Wagner-Döbler I, Cypionka H. Oxidative stress and starvation in Dinoroseobacter shibae: the role of extrachromosomal elements. Front Microbiol 2015; 6:233. [PMID: 25859246 PMCID: PMC4373377 DOI: 10.3389/fmicb.2015.00233] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/10/2015] [Indexed: 12/31/2022] Open
Abstract
Aerobic anoxygenic phototrophic bacteria (AAP) are abundant in the photic zone of the marine environment. Dinoroseobacter shibae, a representative of the Roseobacter group, converts light into additional energy that enhances its survival especially under starvation. However, light exposure results in the production of cytotoxic reactive oxygen species in AAPs. Here we investigated the response of D. shibae to starvation and oxidative stress, focusing on the role of extrachromosomal elements (ECRs). D. shibae possessing five ECRs (three plasmids and two chromids) was starved for 4 weeks either in the dark or under light/dark cycles and the survival was monitored. Transcriptomics showed that on the chromosome genes with a role in oxidative stress response and photosynthesis were differentially expressed during the light period. Most extrachromosomal genes in contrast showed a general loss of transcriptional activity, especially in dark-starved cells. The observed decrease of gene expression was not due to plasmid loss, as all five ECRs were maintained in the cells. Interestingly, the genes on the 72-kb chromid were the least downregulated, and one region with genes of the oxygen stress response and a light-dependent protochlorophyllide reductase of cyanobacterial origin was strongly activated under the light/dark cycle. A Δ72-kb curing mutant lost the ability to survive under starvation in a light/dark cycle demonstrating the essential role of this chromid for adaptation to starvation and oxidative stress. Our data moreover suggest that the other four ECRs of D. shibae have no vital function under the investigated conditions and therefore were transcriptionally silenced.
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Affiliation(s)
- Maya Soora
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky University of Oldenburg Oldenburg, Germany
| | - Jürgen Tomasch
- Group Microbial Communication, Helmholtz-Centre for Infection Research Braunschweig, Germany
| | - Hui Wang
- Group Microbial Communication, Helmholtz-Centre for Infection Research Braunschweig, Germany
| | - Victoria Michael
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Jörn Petersen
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Bert Engelen
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky University of Oldenburg Oldenburg, Germany
| | - Irene Wagner-Döbler
- Group Microbial Communication, Helmholtz-Centre for Infection Research Braunschweig, Germany
| | - Heribert Cypionka
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky University of Oldenburg Oldenburg, Germany
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Dai J, Wei H, Tian C, Damron FH, Zhou J, Qiu D. An extracytoplasmic function sigma factor-dependent periplasmic glutathione peroxidase is involved in oxidative stress response of Shewanella oneidensis. BMC Microbiol 2015; 15:34. [PMID: 25887418 PMCID: PMC4336711 DOI: 10.1186/s12866-015-0357-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/20/2015] [Indexed: 11/30/2022] Open
Abstract
Background Bacteria use alternative sigma factors (σs) to regulate condition-specific gene expression for survival and Shewanella harbors multiple ECF (extracytoplasmic function) σ genes and cognate anti-sigma factor genes. Here we comparatively analyzed two of the rpoE-like operons in the strain MR-1: rpoE-rseA-rseB-rseC and rpoE2-chrR. Results RpoE was important for bacterial growth at low and high temperatures, in the minimal medium, and high salinity. The degP/htrA orthologue, required for growth of Escherichia coli and Pseudomonas aeruginosa at high temperature, is absent in Shewanella, while the degQ gene is RpoE-regulated and is required for bacterial growth at high temperature. RpoE2 was essential for the optimal growth in oxidative stress conditions because the rpoE2 mutant was sensitive to hydrogen peroxide and paraquat. The operon encoding a ferrochelatase paralogue (HemH2) and a periplasmic glutathione peroxidase (PgpD) was identified as RpoE2-dependent. PgpD exhibited higher activities and played a more important role in the oxidative stress responses than the cytoplasmic glutathione peroxidase CgpD under tested conditions. The rpoE2-chrR operon and the identified regulon genes, including pgpD and hemH2, are coincidently absent in several psychrophilic and/or deep-sea Shewanella strains. Conclusion In S. oneidensis MR-1, the RpoE-dependent degQ gene is required for optimal growth under high temperature. The rpoE2 and RpoE2-dependent pgpD gene encoding a periplasmic glutathione peroxidase are involved in oxidative stress responses. But rpoE2 is not required for bacterial growth at low temperature and it even affected bacterial growth under salt stress, indicating that there is a tradeoff between the salt resistance and RpoE2-mediated oxidative stress responses. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0357-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingcheng Dai
- Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuchang District, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hehong Wei
- Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuchang District, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chunyuan Tian
- School of Life Sciences and Technology, Hubei University of Engineering, 272 Jiaotong Avenue, Xiaogan, 432000, China.
| | - Fredrick Heath Damron
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, 22908, USA.
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Botany and Microbiology, The University of Oklahoma, Stephenson Research and Technology Center, 101 David L. Boren Blvd, Norman, OK 73019, USA.
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuchang District, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Laloi C, Havaux M. Key players of singlet oxygen-induced cell death in plants. FRONTIERS IN PLANT SCIENCE 2015; 6:39. [PMID: 25699067 PMCID: PMC4316694 DOI: 10.3389/fpls.2015.00039] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/15/2015] [Indexed: 05/03/2023]
Abstract
The production of reactive oxygen species (ROS) is an unavoidable consequence of oxygenic photosynthesis. Singlet oxygen ((1)O2) is a highly reactive species to which has been attributed a major destructive role during the execution of ROS-induced cell death in photosynthetic tissues exposed to excess light. The study of the specific biological activity of (1)O2 in plants has been hindered by its high reactivity and short lifetime, the concurrent production of other ROS under photooxidative stress, and limited in vivo detection methods. However, during the last 15 years, the isolation and characterization of two (1)O2-overproducing mutants in Arabidopsis thaliana, flu and ch1, has allowed the identification of genetically controlled (1)O2 cell death pathways and a (1)O2 acclimation pathway that are triggered at sub-cytotoxic concentrations of (1)O2. The study of flu has revealed the control of cell death by the plastid proteins EXECUTER (EX)1 and EX2. In ch1, oxidized derivatives of β-carotene, such as β-cyclocitral and dihydroactinidiolide, have been identified as important upstream messengers in the (1)O2 signaling pathway that leads to stress acclimation. In both the flu and ch1 mutants, phytohormones act as important promoters or inhibitors of cell death. In particular, jasmonate has emerged as a key player in the decision between acclimation and cell death in response to (1)O2. Although the flu and ch1 mutants show many similarities, especially regarding their gene expression profiles, key differences, such as EXECUTER-independent cell death in ch1, have also been observed and will need further investigation to be fully understood.
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Affiliation(s)
- Christophe Laloi
- Laboratoire de Génétique et Biophysique des Plantes, Institut de Biologie Environnementale et Biotechnologie, Commissariat à l’Énergie Atomique et aux Énergies AlternativesMarseille, France
- CNRS, UMR 7265 Biologie Végétale et Microbiologie EnvironnementalesMarseille, France
- Aix Marseille UniversitéMarseille, France
- *Correspondence: Christophe Laloi, Laboratoire de Génétique et Biophysique des Plantes, Institut de Biologie Environnementale et Biotechnologie, Commissariat à l’Énergie Atomique et aux nergies Alternatives, F -13009 Marseille, France e-mail: ; Michel Havaux, Laboratoire d’Ecophysiologie Moléculaire des Plantes, Institut de Biologie Environnementale et Biotechnologie, Commissariat à l’Énergie Atomique et aux Énergies Alternatives, F-13108 Saint-Paul-lez-Durance, France e-mail:
| | - Michel Havaux
- CNRS, UMR 7265 Biologie Végétale et Microbiologie EnvironnementalesMarseille, France
- Aix Marseille UniversitéMarseille, France
- Laboratoire d’Ecophysiologie Moléculaire des Plantes, Institut de Biologie Environnementale et Biotechnologie, Commissariat à l’Énergie Atomique et aux Énergies AlternativesSaint-Paul-lez-Durance, France
- *Correspondence: Christophe Laloi, Laboratoire de Génétique et Biophysique des Plantes, Institut de Biologie Environnementale et Biotechnologie, Commissariat à l’Énergie Atomique et aux nergies Alternatives, F -13009 Marseille, France e-mail: ; Michel Havaux, Laboratoire d’Ecophysiologie Moléculaire des Plantes, Institut de Biologie Environnementale et Biotechnologie, Commissariat à l’Énergie Atomique et aux Énergies Alternatives, F-13108 Saint-Paul-lez-Durance, France e-mail:
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Peña-Castillo L, Mercer RG, Gurinovich A, Callister SJ, Wright AT, Westbye AB, Beatty JT, Lang AS. Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides. BMC Genomics 2014; 15:730. [PMID: 25164283 PMCID: PMC4158056 DOI: 10.1186/1471-2164-15-730] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 08/21/2014] [Indexed: 01/05/2023] Open
Abstract
Background The genus Rhodobacter contains purple nonsulfur bacteria found mostly in freshwater environments. Representative strains of two Rhodobacter species, R. capsulatus and R. sphaeroides, have had their genomes fully sequenced and both have been the subject of transcriptional profiling studies. Gene co-expression networks can be used to identify modules of genes with similar expression profiles. Functional analysis of gene modules can then associate co-expressed genes with biological pathways, and network statistics can determine the degree of module preservation in related networks. In this paper, we constructed an R. capsulatus gene co-expression network, performed functional analysis of identified gene modules, and investigated preservation of these modules in R. capsulatus proteomics data and in R. sphaeroides transcriptomics data. Results The analysis identified 40 gene co-expression modules in R. capsulatus. Investigation of the module gene contents and expression profiles revealed patterns that were validated based on previous studies supporting the biological relevance of these modules. We identified two R. capsulatus gene modules preserved in the protein abundance data. We also identified several gene modules preserved between both Rhodobacter species, which indicate that these cellular processes are conserved between the species and are candidates for functional information transfer between species. Many gene modules were non-preserved, providing insight into processes that differentiate the two species. In addition, using Local Network Similarity (LNS), a recently proposed metric for expression divergence, we assessed the expression conservation of between-species pairs of orthologs, and within-species gene-protein expression profiles. Conclusions Our analyses provide new sources of information for functional annotation in R. capsulatus because uncharacterized genes in modules are now connected with groups of genes that constitute a joint functional annotation. We identified R. capsulatus modules enriched with genes for ribosomal proteins, porphyrin and bacteriochlorophyll anabolism, and biosynthesis of secondary metabolites to be preserved in R. sphaeroides whereas modules related to RcGTA production and signalling showed lack of preservation in R. sphaeroides. In addition, we demonstrated that network statistics may also be applied within-species to identify congruence between mRNA expression and protein abundance data for which simple correlation measurements have previously had mixed results. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-730) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St, John's, NL A1B 3X5, Canada.
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Abstract
Fatty acids play important functional and protective roles in living systems. This paper reports on the synthesis of a previously unidentified 19 carbon furan-containing fatty acid, 10,13-epoxy-11-methyl-octadecadienoate (9-(3-methyl-5-pentylfuran-2-yl)nonanoic acid) (19Fu-FA), in phospholipids from Rhodobacter sphaeroides. We show that 19Fu-FA accumulation is increased in cells containing mutations that increase the transcriptional response of this bacterium to singlet oxygen ((1)O2), a reactive oxygen species generated by energy transfer from one or more light-excited donors to molecular oxygen. We identify a previously undescribed class of S-adenosylmethionine-dependent methylases that convert a phospholipid 18 carbon cis unsaturated fatty acyl chain to a 19 carbon methylated trans unsaturated fatty acyl chain (19M-UFA). We also identify genes required for the O2-dependent conversion of this 19M-UFA to 19Fu-FA. Finally, we show that the presence of (1)O2 leads to turnover of 19Fu-Fa in vivo. We propose that furan-containing fatty acids like 19Fu-FA can act as a membrane-bound scavenger of (1)O2, which is naturally produced by integral membrane enzymes of the R. sphaeroides photosynthetic apparatus.
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Wakao S, Chin BL, Ledford HK, Dent RM, Casero D, Pellegrini M, Merchant SS, Niyogi KK. Phosphoprotein SAK1 is a regulator of acclimation to singlet oxygen in Chlamydomonas reinhardtii. eLife 2014; 3:e02286. [PMID: 24859755 PMCID: PMC4067076 DOI: 10.7554/elife.02286] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 05/22/2014] [Indexed: 01/07/2023] Open
Abstract
Singlet oxygen is a highly toxic and inevitable byproduct of oxygenic photosynthesis. The unicellular green alga Chlamydomonas reinhardtii is capable of acclimating specifically to singlet oxygen stress, but the retrograde signaling pathway from the chloroplast to the nucleus mediating this response is unknown. Here we describe a mutant, singlet oxygen acclimation knocked-out 1 (sak1), that lacks the acclimation response to singlet oxygen. Analysis of genome-wide changes in RNA abundance during acclimation to singlet oxygen revealed that SAK1 is a key regulator of the gene expression response during acclimation. The SAK1 gene encodes an uncharacterized protein with a domain conserved among chlorophytes and present in some bZIP transcription factors. The SAK1 protein is located in the cytosol, and it is induced and phosphorylated upon exposure to singlet oxygen, suggesting that it is a critical intermediate component of the retrograde signal transduction pathway leading to singlet oxygen acclimation.DOI: http://dx.doi.org/10.7554/eLife.02286.001.
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Affiliation(s)
- Setsuko Wakao
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Brian L Chin
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Heidi K Ledford
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Rachel M Dent
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - David Casero
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, United States
| | - Sabeeha S Merchant
- Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, United States Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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