1
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Chen X, Zhao Y, Huang S, Peñuelas J, Sardans J, Wang L, Zheng B. Genome-based identification of phosphate-solubilizing capacities of soil bacterial isolates. AMB Express 2024; 14:85. [PMID: 39078439 PMCID: PMC11289785 DOI: 10.1186/s13568-024-01745-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/17/2024] [Indexed: 07/31/2024] Open
Abstract
Identifying genomic markers for phosphate-solubilizing bacteria (PSB) is vital for advancing agricultural sustainability. This study utilizes whole-genome sequencing and comprehensive bioinformatics analysis, examining the genomes of 76 PSB strains with the aid of specialized genomic databases and analytical tools. We have identified the pqq gene cluster, particularly the pqqC gene, as a key marker for (P) solubilization capabilities. The pqqC gene encodes an enzyme that catalyzes the conversion of precursors to 2-keto-D-gluconic acid, which significantly enhances P solubilization in soil. This gene's importance lies not only in its biochemical function but also in its prevalence and effectiveness across various PSB strains, distinguishing it from other potential markers. Our study focuses on Burkholderia cepacia 51-Y1415, known for its potent solubilization activity, and demonstrates a direct correlation between the abundance of the pqqC gene, the quantitative release of P, and the production of 2-keto-D-gluconic acid over a standard 144-h cultivation period under standardized conditions. This research not only underscores the role of the pqqC gene as a universal marker for the rapid screening and functional annotation of PSB strains but also highlights its implications for enhancing soil fertility and crop yields, thereby contributing to more sustainable agricultural practices. Our findings provide a foundation for future research aimed at developing targeted strategies to optimize phosphate solubilization, suggesting areas for further investigation such as the integration of these genomic insights into practical agricultural applications to maximize the effectiveness of PSB strains in real-world soil environments.
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Affiliation(s)
- Xiaoqing Chen
- School of Environmental Science and Engineering, Xiamen University of Technology, Xiamen, 361024, People's Republic of China
- Xiamen Key Laboratory of Membrane Research and Application, Xiamen, 361024, People's Republic of China
| | - Yiting Zhao
- School of Environmental Science and Engineering, Xiamen University of Technology, Xiamen, 361024, People's Republic of China
| | - Shasha Huang
- School of Environmental Science and Engineering, Xiamen University of Technology, Xiamen, 361024, People's Republic of China
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Catalonia, 08193, Bellaterra, Spain
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain
| | - Jordi Sardans
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Catalonia, 08193, Bellaterra, Spain
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain
| | - Lei Wang
- School of Environmental Science and Engineering, Xiamen University of Technology, Xiamen, 361024, People's Republic of China
| | - Bangxiao Zheng
- School of Environmental Science and Engineering, Xiamen University of Technology, Xiamen, 361024, People's Republic of China.
- Xiamen Key Laboratory of Membrane Research and Application, Xiamen, 361024, People's Republic of China.
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2
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Zhu W, Iavarone AT, Klinman JP. Hydrogen-Deuterium Exchange Mass Spectrometry Identifies Local and Long-Distance Interactions within the Multicomponent Radical SAM Enzyme, PqqE. ACS CENTRAL SCIENCE 2024; 10:251-263. [PMID: 38435514 PMCID: PMC10906245 DOI: 10.1021/acscentsci.3c01023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 03/05/2024]
Abstract
Interactions among proteins and peptides are essential for many biological activities including the tailoring of peptide substrates to produce natural products. The first step in the production of the bacterial redox cofactor pyrroloquinoline quinone (PQQ) from its peptide precursor is catalyzed by a radical SAM (rSAM) enzyme, PqqE. We describe the use of hydrogen-deuterium exchange mass spectrometry (HDX-MS) to characterize the structure and conformational dynamics in the protein-protein and protein-peptide complexes necessary for PqqE function. HDX-MS-identified hotspots can be discerned in binary and ternary complex structures composed of the peptide PqqA, the peptide-binding chaperone PqqD, and PqqE. Structural conclusions are supported by size-exclusion chromatography coupled to small-angle X-ray scattering (SEC-SAXS). HDX-MS further identifies reciprocal changes upon the binding of substrate peptide and S-adenosylmethionine (SAM) to the PqqE/PqqD complex: long-range conformational alterations have been detected upon the formation of a quaternary complex composed of PqqA/PqqD/PqqE and SAM, spanning nearly 40 Å, from the PqqA binding site in PqqD to the PqqE active site Fe4S4. Interactions among the various regions are concluded to arise from both direct contact and distal communication. The described experimental approach can be readily applied to the investigation of protein conformational communication among a large family of peptide-modifying rSAM enzymes.
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Affiliation(s)
- Wen Zhu
- Department
of Chemistry and Biochemistry, Florida State
University, Tallahassee, Florida 32306, United States
- California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
| | - Anthony T. Iavarone
- California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
| | - Judith P. Klinman
- California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
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3
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Gao H, Wang Y, Yang J, Qiu M, Lei Z, Zhang W, Jiang W, Xin F, Jiang M. Microbial synthesis of pyrroloquinoline quinone. World J Microbiol Biotechnol 2023; 40:31. [PMID: 38057682 DOI: 10.1007/s11274-023-03833-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023]
Abstract
Pyrroloquinoline quinone (PQQ) is a peptide-modified natural product. PQQ has important physiological functions such as anti-oxidation, anti-aging, and immunity enhancement. However, due to the lack of in-depth understanding of PQQ biosynthesis and regulation, inefficient PQQ production level limits its wide application. Accordingly, there is still an urgent need to develop high-yielding strains for synthesis of PQQ. This paper reviewed the research and development trends on the PQQ biosynthetic pathways, catalytic reaction mechanism of key enzymes, and the selection of high-yielding strains, which also prospects for the future construction of PQQ biosynthetic microbial cell factories.
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Affiliation(s)
- Hao Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Yingshan Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Jiahui Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Min Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Zhixiao Lei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
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4
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Lo SC, Tsai SY, Chang WH, Wu IC, Sou NL, Hung SHW, Chiang EPI, Huang CC. Characterization of the Pyrroloquinoline Quinone Producing Rhodopseudomonas palustris as a Plant Growth-Promoting Bacterium under Photoautotrophic and Photoheterotrophic Culture Conditions. Int J Mol Sci 2023; 24:14080. [PMID: 37762380 PMCID: PMC10531626 DOI: 10.3390/ijms241814080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Rhodopseudomonas palustris is a purple non-sulfide bacterium (PNSB), and some strains have been proven to promote plant growth. However, the mechanism underlying the effect of these PNSBs remains limited. Based on genetic information, R. palustris possesses the ability to produce pyrroloquinoline quinone (PQQ). PQQ is known to play a crucial role in stimulating plant growth, facilitating phosphorous solubilization, and acting as a reactive oxygen species scavenger. However, it is still uncertain whether growth conditions influence R. palustris's production of PQQ and other characteristics. In the present study, it was found that R. palustris exhibited a higher expression of genes related to PQQ synthesis under autotrophic culture conditions as compared to acetate culture conditions. Moreover, similar patterns were observed for phosphorous solubilization and siderophore activity, both of which are recognized to contribute to plant-growth benefits. However, these PNSB culture conditions did not show differences in Arabidopsis growth experiments, indicating that there may be other factors influencing plant growth in addition to PQQ content. Furthermore, the endophytic bacterial strains isolated from Arabidopsis exhibited differences according to the PNSB culture conditions. These findings imply that, depending on the PNSB's growing conditions, it may interact with various soil bacteria and facilitate their infiltration into plants.
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Affiliation(s)
- Shou-Chen Lo
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-C.L.); (S.-Y.T.); (W.-H.C.); (I.-C.W.); (S.-H.W.H.)
| | - Shang-Yieng Tsai
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-C.L.); (S.-Y.T.); (W.-H.C.); (I.-C.W.); (S.-H.W.H.)
| | - Wei-Hsiang Chang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-C.L.); (S.-Y.T.); (W.-H.C.); (I.-C.W.); (S.-H.W.H.)
| | - I-Chen Wu
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-C.L.); (S.-Y.T.); (W.-H.C.); (I.-C.W.); (S.-H.W.H.)
| | - Nga-Lai Sou
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 402202, Taiwan; (N.-L.S.); (E.-P.I.C.)
| | - Shih-Hsun Walter Hung
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-C.L.); (S.-Y.T.); (W.-H.C.); (I.-C.W.); (S.-H.W.H.)
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
| | - En-Pei Isabel Chiang
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 402202, Taiwan; (N.-L.S.); (E.-P.I.C.)
- Program in Microbial Genomics, National Chung Hsing University, Taichung 402202, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402202, Taiwan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-C.L.); (S.-Y.T.); (W.-H.C.); (I.-C.W.); (S.-H.W.H.)
- Program in Microbial Genomics, National Chung Hsing University, Taichung 402202, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402202, Taiwan
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5
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Krüsemann JL, Rainaldi V, Cotton CA, Claassens NJ, Lindner SN. The cofactor challenge in synthetic methylotrophy: bioengineering and industrial applications. Curr Opin Biotechnol 2023; 82:102953. [PMID: 37320962 DOI: 10.1016/j.copbio.2023.102953] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/03/2023] [Accepted: 05/14/2023] [Indexed: 06/17/2023]
Abstract
Methanol is a promising feedstock for industrial bioproduction: it can be produced renewably and has high solubility and limited microbial toxicity. One of the key challenges for its bio-industrial application is the first enzymatic oxidation step to formaldehyde. This reaction is catalysed by methanol dehydrogenases (MDH) that can use NAD+, O2 or pyrroloquinoline quinone (PQQ) as an electron acceptor. While NAD-dependent MDH are simple to express and have the highest energetic efficiency, they exhibit mediocre kinetics and poor thermodynamics at ambient temperatures. O2-dependent methanol oxidases require high oxygen concentrations, do not conserve energy and thus produce excessive heat as well as toxic H2O2. PQQ-dependent MDH provide a good compromise between energy efficiency and good kinetics that support fast growth rates without any drawbacks for process engineering. Therefore, we argue that this enzyme class represents a promising solution for industry and outline engineering strategies for the implementation of these complex systems in heterologous hosts.
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Affiliation(s)
- Jan L Krüsemann
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry and Synthetic Metabolism, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Vittorio Rainaldi
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | | | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Steffen N Lindner
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany.
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6
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Šigutová H, Šigut M, Pyszko P, Kostovčík M, Kolařík M, Drozd P. Seasonal Shifts in Bacterial and Fungal Microbiomes of Leaves and Associated Leaf-Mining Larvae Reveal Persistence of Core Taxa Regardless of Diet. Microbiol Spectr 2023; 11:e0316022. [PMID: 36629441 PMCID: PMC9927363 DOI: 10.1128/spectrum.03160-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
Microorganisms are key mediators of interactions between insect herbivores and their host plants. Despite a substantial interest in studying various aspects of these interactions, temporal variations in microbiomes of woody plants and their consumers remain understudied. In this study, we investigated shifts in the microbiomes of leaf-mining larvae (Insecta: Lepidoptera) and their host trees over one growing season in a deciduous temperate forest. We used 16S and ITS2 rRNA gene metabarcoding to profile the bacterial and fungal microbiomes of leaves and larvae. We found pronounced shifts in the leaf and larval microbiota composition and richness as the season progressed, and bacteria and fungi showed consistent patterns. The quantitative similarity between leaf and larval microbiota was very low for bacteria (~9%) and decreased throughout the season, whereas fungal similarity increased and was relatively high (~27%). In both leaves and larvae, seasonality, along with host taxonomy, was the most important factor shaping microbial communities. We identified frequently occurring microbial taxa with significant seasonal trends, including those more prevalent in larvae (Streptococcus, Candida sake, Debaryomyces prosopidis, and Neoascochyta europaea), more prevalent in leaves (Erwinia, Seimatosporium quercinum, Curvibasidium cygneicollum, Curtobacterium, Ceramothyrium carniolicum, and Mycosphaerelloides madeirae), and frequent in both leaves and larvae (bacterial strain P3OB-42, Methylobacterium/Methylorubrum, Bacillus, Acinetobacter, Cutibacterium, and Botrytis cinerea). Our results highlight the importance of considering seasonality when studying the interactions between plants, herbivorous insects, and their respective microbiomes, and illustrate a range of microbial taxa persistent in larvae, regardless of their occurrence in the diet. IMPORTANCE Leaf miners are endophagous insect herbivores that feed on plant tissues and develop and live enclosed between the epidermis layers of a single leaf for their entire life cycle. Such close association is a precondition for the evolution of more intimate host-microbe relationships than those found in free-feeding herbivores. Simultaneous comparison of bacterial and fungal microbiomes of leaves and their tightly linked consumers over time represents an interesting study system that could fundamentally contribute to the ongoing debate on the microbial residence of insect gut. Furthermore, leaf miners are ideal model organisms for interpreting the ecological and evolutionary roles of microbiota in host plant specialization. In this study, the larvae harbored specific microbial communities consisting of core microbiome members. Observed patterns suggest that microbes, especially bacteria, may play more important roles in the caterpillar holobiont than generally presumed.
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Affiliation(s)
- Hana Šigutová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Šigut
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Petr Pyszko
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Kostovčík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Miroslav Kolařík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Pavel Drozd
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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7
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Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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8
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Xue D, Older EA, Zhong Z, Shang Z, Chen N, Dittenhauser N, Hou L, Cai P, Walla MD, Dong SH, Tang X, Chen H, Nagarkatti P, Nagarkatti M, Li YX, Li J. Correlational networking guides the discovery of unclustered lanthipeptide protease-encoding genes. Nat Commun 2022; 13:1647. [PMID: 35347143 PMCID: PMC8960859 DOI: 10.1038/s41467-022-29325-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/21/2022] [Indexed: 11/09/2022] Open
Abstract
Bacterial natural product biosynthetic genes, canonically clustered, have been increasingly found to rely on hidden enzymes encoded elsewhere in the genome for completion of biosynthesis. The study and application of lanthipeptides are frequently hindered by unclustered protease genes required for final maturation. Here, we establish a global correlation network bridging the gap between lanthipeptide precursors and hidden proteases. Applying our analysis to 161,954 bacterial genomes, we establish 5209 correlations between precursors and hidden proteases, with 91 prioritized. We use network predictions and co-expression analysis to reveal a previously missing protease for the maturation of class I lanthipeptide paenilan. We further discover widely distributed bacterial M16B metallopeptidases of previously unclear biological function as a new family of lanthipeptide proteases. We show the involvement of a pair of bifunctional M16B proteases in the production of previously unreported class III lanthipeptides with high substrate specificity. Together, these results demonstrate the strength of our correlational networking approach to the discovery of hidden lanthipeptide proteases and potentially other missing enzymes for natural products biosynthesis.
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Affiliation(s)
- Dan Xue
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Ethan A Older
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Zheng Zhong
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhuo Shang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Nanzhu Chen
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Nolan Dittenhauser
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Lukuan Hou
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Peiyan Cai
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Michael D Walla
- The Mass Spectrometry Center, Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Shi-Hui Dong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Hexin Chen
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Yong-Xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA.
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9
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Xu M, Xu Q, Wang M, Qiu S, Xu D, Zhang W, Wang W, He J, Wang Q, Ran T, Sun B. Crystal structures of TTHA1265 and TTHA1264/TTHA1265 complex reveal an intrinsic heterodimeric assembly. Int J Biol Macromol 2022; 207:424-433. [PMID: 35276293 DOI: 10.1016/j.ijbiomac.2022.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 11/05/2022]
Abstract
Zinc peptidase M16 family members are widely distributed in most prokaryotic and eukaryotic organisms. M16 family has been divided into three subfamilies, M16A, M16B and M16C, based on sequence alignments and subunit connectivity. TTHA1264, an M16B protein found in Thermus thermophiles HB8, possesses an HXXEH motif essential for Zn2+ binding and catalytic activity. TTHA1265 is another member of M16B, which lacks the metal-binding motif but with a conserved active-site R/Y pair commonly found in the C-terminal half of M16 enzymes. Sequence analysis showed that two genes coding for TTHA1264 and TTHA1265 assemble into a single operon in the bacterial genome. Here, we report the crystal structure of TTHA1265 and TTHA1264/TTHA1265 complex from T. thermophilus HB8. Interestingly, when TTHA1264 and TTHA1265 are present alone, TTHA1264 forms a monomer, TTHA1265 forms a homodimer, respectively. However, TTHA264 and TTHA1265 assembled into a heterodimeric complex, indicating that they prefer to form heterodimer. Biochemical data further confirmed the heterodimeric assembly indicating intrinsic heterodimeric assembly of TTHA1264 and TTHA1265. This property of TTHA1264 and TTHA1265 is consistent with the characteristics of the M16B family.
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Affiliation(s)
- Mengxue Xu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Qin Xu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Shenshen Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Dongqing Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Weizhe Zhang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Weiwu Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jianhua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qisheng Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
| | - Tingting Ran
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Bo Sun
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
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10
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Abstract
The widely distributed, essential redox factor pyrroloquinoline quinone (PQQ, methoxatin) (1) was discovered in the mid-1960s. The breadth and depth of its biological effects are steadily being revealed, and understanding its biosynthesis at the genomic level is a continuing process. In this review, aspects of the chemistry, biology, biosynthesis, and commercial production of 1 at the gene level, and some applications, are presented from discovery through to mid-2021.
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Affiliation(s)
- Geoffrey A Cordell
- Natural Products Inc., Evanston, Illinois 60202, United States.,Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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11
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Generation of a Gluconobacter oxydans knockout collection for improved extraction of rare earth elements. Nat Commun 2021; 12:6693. [PMID: 34795278 PMCID: PMC8602642 DOI: 10.1038/s41467-021-27047-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/27/2021] [Indexed: 11/28/2022] Open
Abstract
Bioleaching of rare earth elements (REEs), using microorganisms such as Gluconobacter oxydans, offers a sustainable alternative to environmentally harmful thermochemical extraction, but is currently not very efficient. Here, we generate a whole-genome knockout collection of single-gene transposon disruption mutants for G. oxydans B58, to identify genes affecting the efficacy of REE bioleaching. We find 304 genes whose disruption alters the production of acidic biolixiviant. Disruption of genes underlying synthesis of the cofactor pyrroloquinoline quinone (PQQ) and the PQQ-dependent membrane-bound glucose dehydrogenase nearly eliminates bioleaching. Disruption of phosphate-specific transport system genes enhances bioleaching by up to 18%. Our results provide a comprehensive roadmap for engineering the genome of G. oxydans to further increase its bioleaching efficiency.
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Zhao C, Wan Y, Cao X, Zhang H, Bao X. Comparative genomics and analysis of the mechanism of PQQ overproduction in Methylobacterium. World J Microbiol Biotechnol 2021; 37:100. [PMID: 33983497 DOI: 10.1007/s11274-021-03068-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/06/2021] [Indexed: 11/24/2022]
Abstract
Methylobacterium sp. CLZ was isolated from soil contaminated with chemical wastewater. This strain simultaneously synthesizes Pyrroloquinoline quinone (PQQ), Coenzyme Q10 (CoQ10), and carotenoids by utilizing methanol as a carbon source. Comparative genomic analysis was performed for five Methylobacterium strains. As per the outcomes, the Methylobacterium CLZ strain showed the smallest genome size and the lowest number of proteins. Thus, it can serve as an ideal cell model for investigating the biological process of Methylobacterium and constructing genetically engineered Methylobacterium. The Methylobacterium CLZ strain's pqqL gene, which does not occur in other Methylobacterium strains but plays a crucial role in PQQ synthesis. This was a surprising finding for the study of PQQ biosynthesis in Methylobacterium. Methylobacterium sp. NI91 strain was generated by random mutagenesis of CLZ strain, and NI91 strain showed a 72.44% increase in PQQ yield. The mutation in the mxaJ gene involved in the methanol dehydrogenase (MDH) synthesis was identified through comparative genomic analysis of the whole genome of mutant strain NI91 and wild-type strain CLZ. The mxaJ gene was found to be upregulated in the NI91 strain. Thus, the up-regulation of the mxaJ gene could be correlated with the high yield of PQQ, and it could provide valuable clues for strain engineering to improve PQQ production.
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Affiliation(s)
- Changle Zhao
- College of Life Sciences, Shihezi University, Shihezi, 832003, People's Republic of China
| | - Yinping Wan
- College of Life Sciences, Shihezi University, Shihezi, 832003, People's Republic of China
| | - Xiaojie Cao
- College of Life Sciences, Shihezi University, Shihezi, 832003, People's Republic of China
| | - Huili Zhang
- College of Life Sciences, Shihezi University, Shihezi, 832003, People's Republic of China.
| | - Xin Bao
- Xinjiang Fufeng Biotechnology Co., Ltd., Ürümqi, 830001, Xinjiang, People's Republic of China
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 393] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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14
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Zhu W, Klinman JP. Biogenesis of the peptide-derived redox cofactor pyrroloquinoline quinone. Curr Opin Chem Biol 2020; 59:93-103. [PMID: 32731194 PMCID: PMC7736144 DOI: 10.1016/j.cbpa.2020.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022]
Abstract
Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes that also plays beneficial roles in organisms from other kingdoms. We review recent developments on the pathway of PQQ biogenesis, focusing on the mechanisms of PqqE, PqqF/G, and PqqB. These advances may shed light on other, uncharacterized biosynthetic pathways.
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Affiliation(s)
- Wen Zhu
- California Institute for Quantitative Biosciences and Department of Chemistry, University of California, Berkeley, CA, 94720-3220, USA
| | - Judith P Klinman
- California Institute for Quantitative Biosciences and Department of Chemistry, University of California, Berkeley, CA, 94720-3220, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720-3220, USA.
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15
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Wang G, Zhou Y, Ma K, Zhang F, Ye J, Zhong G, Yang X. Bioconversion of recombinantly produced precursor peptide pqqA into pyrroloquinoline quinone (PQQ) using a cell-free in vitro system. Protein Expr Purif 2020; 178:105777. [PMID: 33069826 DOI: 10.1016/j.pep.2020.105777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 01/11/2023]
Abstract
Pyrroloquinoline quinone (PQQ) has been recognized as the third class of redox cofactors in addition to the well-known nicotinamides (NAD(P)+) and flavins (FAD, FMN). It plays important physiological roles in various organisms and has strong antioxidant properties. The biosynthetic pathway of PQQ involves a gene cluster composed of 4-7 genes, named pqqA-G, among which pqqA is a key gene for PQQ synthesis, encoding the precursor peptide PqqA. To produce recombinant PqqA in E. coli, fusion tags were used to increase the stability and solubility of the peptide, as well simplify the scale-up of the fermentation process. In this paper, pqqA from Gluconobacter oxydans 621H was expressed in E. coli BL21 (DE3) as a fusion protein with SUMO and purified using a hexahistidine (His6) tag. The SUMO fusion protein and His6 tag were specifically recognized and cleaved by the SUMO specific ULP protease, and immobilized-metal affinity chromatography was used to obtain high-purity precursor peptide PqqA. Expression and purification of target proteins was confirmed by Tricine-SDS-PAGE. Finally, the synthesis of PQQ in a cell-free enzymatic reaction in vitro was confirmed by LC-MS.
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Affiliation(s)
- Guanglu Wang
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China
| | - Yifei Zhou
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China
| | - Ke Ma
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China
| | - Fan Zhang
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China
| | - Jianbin Ye
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China
| | - Guifang Zhong
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China
| | - Xuepeng Yang
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China.
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16
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Roszczenko-Jasińska P, Vu HN, Subuyuj GA, Crisostomo RV, Cai J, Lien NF, Clippard EJ, Ayala EM, Ngo RT, Yarza F, Wingett JP, Raghuraman C, Hoeber CA, Martinez-Gomez NC, Skovran E. Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1. Sci Rep 2020; 10:12663. [PMID: 32728125 PMCID: PMC7391723 DOI: 10.1038/s41598-020-69401-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/09/2020] [Indexed: 11/08/2022] Open
Abstract
Lanthanide elements have been recently recognized as "new life metals" yet much remains unknown regarding lanthanide acquisition and homeostasis. In Methylorubrum extorquens AM1, the periplasmic lanthanide-dependent methanol dehydrogenase XoxF1 produces formaldehyde, which is lethal if allowed to accumulate. This property enabled a transposon mutagenesis study and growth studies to confirm novel gene products required for XoxF1 function. The identified genes encode an MxaD homolog, an ABC-type transporter, an aminopeptidase, a putative homospermidine synthase, and two genes of unknown function annotated as orf6 and orf7. Lanthanide transport and trafficking genes were also identified. Growth and lanthanide uptake were measured using strains lacking individual lanthanide transport cluster genes, and transmission electron microscopy was used to visualize lanthanide localization. We corroborated previous reports that a TonB-ABC transport system is required for lanthanide incorporation to the cytoplasm. However, cells were able to acclimate over time and bypass the requirement for the TonB outer membrane transporter to allow expression of xoxF1 and growth. Transcriptional reporter fusions show that excess lanthanides repress the gene encoding the TonB-receptor. Using growth studies along with energy dispersive X-ray spectroscopy and transmission electron microscopy, we demonstrate that lanthanides are stored as cytoplasmic inclusions that resemble polyphosphate granules.
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Affiliation(s)
- Paula Roszczenko-Jasińska
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, USA
- Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Huong N Vu
- Department of Biological Sciences, San José State University, San José, CA, USA
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Gabriel A Subuyuj
- Department of Biological Sciences, San José State University, San José, CA, USA
- Department of Microbiology and Molecular Genetics, University of California At Davis, Davis, CA, USA
| | - Ralph Valentine Crisostomo
- Department of Biological Sciences, San José State University, San José, CA, USA
- Molecular Biology Institute, University of California At Los Angeles, Los Angeles, CA, USA
| | - James Cai
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Nicholas F Lien
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Erik J Clippard
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Elena M Ayala
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Richard T Ngo
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Fauna Yarza
- Department of Biological Sciences, San José State University, San José, CA, USA
- Department of Biochemistry and Biophysics, University of California At San Francisco, San Francisco, CA, USA
| | - Justin P Wingett
- Department of Biological Sciences, San José State University, San José, CA, USA
| | | | - Caitlin A Hoeber
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Norma C Martinez-Gomez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, USA.
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, California, USA.
| | - Elizabeth Skovran
- Department of Biological Sciences, San José State University, San José, CA, USA.
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17
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Zhu W, Walker LM, Tao L, Iavarone AT, Wei X, Britt RD, Elliott SJ, Klinman JP. Structural Properties and Catalytic Implications of the SPASM Domain Iron-Sulfur Clusters in Methylorubrum extorquens PqqE. J Am Chem Soc 2020; 142:12620-12634. [PMID: 32643933 DOI: 10.1021/jacs.0c02044] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Understanding the relationship between the metallocofactor and its protein environment is the key to uncovering the mechanism of metalloenzymes. PqqE, a radical S-adenosylmethionine enzyme in pyrroloquinoline quinone (PQQ) biosynthesis, contains three iron-sulfur cluster binding sites. Two auxiliary iron-sulfur cluster binding sites, designated as AuxI and AuxII, use distinctive ligands compared to other proteins in the family while their functions remain unclear. Here, we investigate the electronic properties of these iron-sulfur clusters and compare the catalytic efficiency of wild-type (WT) Methylorubrum extorquens AM1 PqqE to a range of mutated constructs. Using native mass spectrometry, protein film electrochemistry, and electron paramagnetic resonance spectroscopy, we confirm the previously proposed incorporation of a mixture of [2Fe-2S] and [4Fe-4S] clusters at the AuxI site and are able to assign redox potentials to each of the three iron-sulfur clusters. Significantly, a conservative mutation at AuxI, C268H, shown to selectively incorporate a [4Fe-4S] cluster, catalyzes an enhancement of uncoupled S-adenosylmethionine cleavage relative to WT, together with the elimination of detectable peptide cross-linked product. While a [4Fe-4S] cluster can be tolerated at the AuxI site, the aggregate findings suggest a functional [2Fe-2S] configuration within the AuxI site. PqqE variants with nondestructive ligand replacements at AuxII also show that the reduction potential at this site can be manipulated by changing the electronegativity of the unique aspartate ligand. A number of novel mechanistic features are proposed based on the kinetic and spectroscopic data. Additionally, bioinformatic analyses suggest that the unique ligand environment of PqqE may be relevant to its role in PQQ biosynthesis within an oxygen-dependent biosynthetic pathway.
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Affiliation(s)
- Wen Zhu
- California Institute for Quantitative Biosciences, University of California-Berkeley, Berkeley, California 94720, United States
| | - Lindsey M Walker
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Lizhi Tao
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Anthony T Iavarone
- California Institute for Quantitative Biosciences, University of California-Berkeley, Berkeley, California 94720, United States
| | - Xuetong Wei
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, United States
| | - R David Britt
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Sean J Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Judith P Klinman
- California Institute for Quantitative Biosciences, University of California-Berkeley, Berkeley, California 94720, United States.,Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, United States.,Department of Chemistry, University of California-Berkeley, Berkeley, California 94720, United States
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