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Sheng Y, Zhang S, Li X, Wang S, Liu T, Wang C, Yan L. Phenotypic and genomic insights into mutant with high nattokinase-producing activity induced by carbon ion beam irradiation of Bacillus subtilis. Int J Biol Macromol 2024; 271:132398. [PMID: 38754670 DOI: 10.1016/j.ijbiomac.2024.132398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Nattokinase (NK) is found in fermented foods and has high fibrinolytic activity, which makes it promising for biological applications. In this study, a mutant strain (Bacillus subtilis ZT-S1, 5529.56 ± 183.59 U/mL) with high NK-producing activity was obtained using 12C6+ heavy ion beam mutagenesis for the first time. The surface morphology of B. subtilis is also altered by changes in functional groups caused by heavy ion beams. Furthermore, B. subtilis ZT-S1 required more carbon and nitrogen sources and reached stabilization phase later. Comparative genome analysis revealed that most of the mutant implicated genes (oppA, appA, kinA, spoIIP) were related to spore formation. And the affected rpoA is related to the synthesis of the NK-coding gene aprE. In addition, the B. subtilis ZT-S1 obtained by mutagenesis had good genetic stability. This study further explores the factors affecting NK activity and provides a promising microbial resource for NK production in commercial applications.
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Affiliation(s)
- Yanan Sheng
- College of Food, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang 163319, China
| | - Xintong Li
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang 163319, China
| | - Shicheng Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang 163319, China
| | - Tao Liu
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang 163319, China
| | - Changyuan Wang
- College of Food, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Lei Yan
- College of Food, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China; Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang 163319, China.
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2
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Ogura M, Matsutani M, Asai K, Suzuki M. Glucose controls manganese homeostasis through transcription factors regulating known and newly identified manganese transporter genes in Bacillus subtilis. J Biol Chem 2023; 299:105069. [PMID: 37468100 PMCID: PMC10448178 DOI: 10.1016/j.jbc.2023.105069] [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: 06/15/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023] Open
Abstract
Mn2+ is an essential nutrient whose concentration is tightly controlled in bacteria. In Bacillus subtilis, the Mn2+-activated transcription factor MntR controls Mn2+ transporter genes. However, factors regulating intracellular Mn2+ concentration are incompletely understood. Here, we found that glucose addition induces an increase in intracellular Mn2+ concentration. We determined this upshift was mediated by glucose induction of the major Mn2+ importer gene mntH by the transcription factor AhrC, which is known to be involved in arginine metabolism and to be indirectly induced by glucose. In addition, we identified novel AhrC-regulated genes encoding the Mn2+ importer YcsG and the ABC-type exporter YknUV. We found the expression of these genes was also regulated by glucose and contributes to the glucose induction of Mn2+ concentrations. ycsG expression is regulated by MntR as well. Furthermore, we analyzed the interaction of AhrC and MntR with the promoter driving ycsG expression and examined the Mn2+-dependent induction of this promoter to identify the transcription factors responsible for the Mn2+ induction. RNA-Seq revealed that disruption of ahrC and mntR affected the expression of 502 and 478 genes, respectively (false discovery rate, <0.001, log2[fold change] ≥ |2|. The AhrC- and/or MntR-dependent expression of twenty promoters was confirmed by LacZ analysis, and AhrC or MntR binding to some of these promoters was observed via EMSA. The finding that glucose promotes an increase in intracellular Mn2+ levels without changes in extracellular Mn2+ concentrations is reasonable for the bacterium, as intracellular Mn2+ is required for enzymes and pathways mediating glucose metabolism.
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Affiliation(s)
- Mitsuo Ogura
- Institute of Oceanic Research and Development, Tokai University, Shizuoka, Japan.
| | | | - Kei Asai
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Michio Suzuki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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3
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Gangwal A, Kumar N, Sangwan N, Dhasmana N, Dhawan U, Sajid A, Arora G, Singh Y. Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages. FEMS Microbiol Rev 2023; 47:fuad044. [PMID: 37533212 PMCID: PMC10465088 DOI: 10.1093/femsre/fuad044] [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] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/04/2023] Open
Abstract
Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein-protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.
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Affiliation(s)
- Aakriti Gangwal
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nishant Kumar
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nitika Sangwan
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Neha Dhasmana
- School of Medicine, New York University, 550 First Avenue New York-10016, New York, United States
| | - Uma Dhawan
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Andaleeb Sajid
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Gunjan Arora
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi-110007, India
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4
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Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C. A model industrial workhorse:
Bacillus subtilis
strain 168 and its genome after a quarter of a century. Microb Biotechnol 2023; 16:1203-1231. [PMID: 37002859 DOI: 10.1111/1751-7915.14257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 04/04/2023] Open
Abstract
The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).
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Affiliation(s)
- Erhard Bremer
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
| | - Alexandra Calteau
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine Hong Kong University Pokfulam SAR Hong Kong China
| | - Colin Harwood
- Centre for Bacterial Cell Biology, Biosciences Institute Newcastle University Baddiley Clark Building Newcastle upon Tyne UK
| | - John D. Helmann
- Department of Microbiology Cornell University Ithaca New York USA
| | - Claudine Médigue
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Bernhard O. Palsson
- Department of Bioengineering University of California San Diego La Jolla USA
| | | | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Abril Zuniga
- Department of Biology San Diego State University San Diego California USA
| | - Cristal Zuniga
- Bioinformatics and Medical Informatics Graduate Program San Diego State University San Diego California USA
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5
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Wicke D, Meißner J, Warneke R, Elfmann C, Stülke J. Understudied proteins and understudied functions in the model bacterium Bacillus subtilis-A major challenge in current research. Mol Microbiol 2023. [PMID: 36882621 DOI: 10.1111/mmi.15053] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/28/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023]
Abstract
Model organisms such as the Gram-positive bacterium Bacillus subtilis have been studied intensively for decades. However, even for model organisms, no function has been identified for about one fourth of all proteins. It has recently been realized that such understudied proteins as well as poorly studied functions set a limitation to our understanding of the requirements for cellular life, and the Understudied Proteins Initiative has been launched. Of poorly studied proteins, those that are strongly expressed are likely to be important to the cell and should therefore be considered high priority in further studies. Since the functional analysis of unknown proteins can be extremely laborious, a minimal knowledge is required prior to targeted functional studies. In this review, we discuss strategies to obtain such a minimal annotation, for example, from global interaction, expression, or localization studies. We present a set of 41 highly expressed and poorly studied proteins of B. subtilis. Several of these proteins are thought or known to bind RNA and/or the ribosome, some may control the metabolism of B. subtilis, and another subset of particularly small proteins may act as regulatory elements to control the expression of downstream genes. Moreover, we discuss the challenges of poorly studied functions with a focus on RNA-binding proteins, amino acid transport, and the control of metabolic homeostasis. The identification of the functions of the selected proteins not only will strongly advance our knowledge on B. subtilis, but also on other organisms since many of the proteins are conserved in many groups of bacteria.
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Affiliation(s)
- Dennis Wicke
- Department of General Microbiology, Georg-August-University Göttingen, GZMB, Göttingen, Germany
| | - Janek Meißner
- Department of General Microbiology, Georg-August-University Göttingen, GZMB, Göttingen, Germany
| | - Robert Warneke
- Department of General Microbiology, Georg-August-University Göttingen, GZMB, Göttingen, Germany
| | - Christoph Elfmann
- Department of General Microbiology, Georg-August-University Göttingen, GZMB, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Georg-August-University Göttingen, GZMB, Göttingen, Germany
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6
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Burroughs A, Aravind L. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. NAR Genom Bioinform 2023; 5:lqad029. [PMID: 36968430 PMCID: PMC10034599 DOI: 10.1093/nargab/lqad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/25/2023] Open
Abstract
The protein-tyrosine/dual-specificity phosphatases and rhodanese domains constitute a sprawling superfamily of Rossmannoid domains that use a conserved active site with a cysteine to catalyze a range of phosphate-transfer, thiotransfer, selenotransfer and redox activities. While these enzymes have been extensively studied in the context of protein/lipid head group dephosphorylation and various thiotransfer reactions, their overall diversity and catalytic potential remain poorly understood. Using comparative genomics and sequence/structure analysis, we comprehensively investigate and develop a natural classification for this superfamily. As a result, we identified several novel clades, both those which retain the catalytic cysteine and those where a distinct active site has emerged in the same location (e.g. diphthine synthase-like methylases and RNA 2' OH ribosyl phosphate transferases). We also present evidence that the superfamily has a wider range of catalytic capabilities than previously known, including a set of parallel activities operating on various sugar/sugar alcohol groups in the context of NAD+-derivatives and RNA termini, and potential phosphate transfer activities involving sugars and nucleotides. We show that such activities are particularly expanded in the RapZ-C-DUF488-DUF4326 clade, defined here for the first time. Some enzymes from this clade are predicted to catalyze novel DNA-end processing activities as part of nucleic-acid-modifying systems that are likely to function in biological conflicts between viruses and their hosts.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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7
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Pan H, Ma B, Wang H, Cui X, Zhang K, Zhao B, Jiang B, Liang Z, Zhang L, Zhang Y. Efficient Enrichment Method for N-Phosphorylation Peptides in Mouse Brain Tissue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:145-148. [PMID: 36637179 DOI: 10.1021/jasms.2c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In addition to O-phosphorylation, protein N-phosphorylation was proven to play important roles in multiple biological processes. Although affinity methods were developed for the enrichment of N-phosphorylation peptides in cells, it was still difficult to enrich N-phosphorylation peptides in tissue due to its complexity. In this study, we established a workflow for the identification of N-phosphorylation peptides in mouse brain tissue by direct enrichment in high concentration urea. In total, 989 N-phosphorylation sites were obtained using 0.5 M urea as enrichment buffer. Among all identified N-phosphorylation sites, the localization probability over 0.75 was as high as 80%, suggesting the reliability of the method. Furthermore, the sequence motif analysis and gene ontology analysis results showed a good match to previous studies. The method was successfully used for N-phosphorylation analysis of mouse hippocampus from Alzheimer's disease model, and 533 N-phosphorylation sites were identified in 5 × FAD mouse hippocampus tissue. Biological process analysis results showed that "brain development", "cellular response to reactive oxygen species", "microtubule cytoskeleton organization", and "peptidyl-serine phosphorylation" were especially enriched in 5 × FAD mouse. It is suggested that N-phosphorylation may be related to Alzheimer's disease in these aspects.
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Affiliation(s)
- Hui Pan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baofu Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - He Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xulian Cui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kun Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Bo Jiang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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8
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Kanesaki Y, Ogura M. RNA-seq analysis identified glucose-responsive genes and YqfO as a global regulator in Bacillus subtilis. BMC Res Notes 2021; 14:450. [PMID: 34906218 PMCID: PMC8670212 DOI: 10.1186/s13104-021-05869-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022] Open
Abstract
Objective We observed that the addition of glucose enhanced the expression of sigX and sigM, encoding extra-cytoplasmic function sigma factors in Bacillus subtilis. Several regulatory factors were identified for this phenomenon, including YqfO, CshA (RNA helicase), and YlxR (nucleoid-associated protein). Subsequently, the relationships among these regulators were analyzed. Among them, YqfO is conserved in many bacterial genomes and may function as a metal ion insertase or metal chaperone, but has been poorly characterized. Thus, to further characterize YqfO, we performed RNA sequencing (RNA-seq) analysis of YqfO in addition to CshA and YlxR. Results We first performed comparative RNA-seq to detect the glucose-responsive genes. Next, to determine the regulatory effects of YqfO in addition to CshA and YlxR, three pairs of comparative RNA-seq analyses were performed (yqfO/wt, cshA/wt, and ylxR/wt). We observed relatively large regulons (approximately 420, 780, and 180 for YqfO, CshA, and YlxR, respectively) and significant overlaps, indicating close relationships among the three regulators. This study is the first to reveal that YqfO functions as a global regulator in B. subtilis. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05869-1.
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Affiliation(s)
- Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Mitsuo Ogura
- Institute of Oceanic Research and Development, Tokai University, 3-20-1 Orido Shimizu-ku, Shizuoka, 424-8610, Japan.
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9
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Ogura M. Identification of transposon-inserted mutations including rnpB::Tn that abolished glucose induction of sigX encoding extracytoplasmic function-sigma factor in Bacillus subtilis. Biosci Biotechnol Biochem 2021; 86:282-285. [PMID: 34864869 DOI: 10.1093/bbb/zbab211] [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: 11/08/2021] [Accepted: 11/27/2021] [Indexed: 11/13/2022]
Abstract
We investigated the regulators of the glucose induction (GI) of the ECF-sigma genes sigX/M. During further screening of transposon-inserted mutants, we identified several regulators including an RNA component of RNase P (rnpB), which is required for tRNA maturation. A depletion of rnpB is known to trigger the stringent response. We showed evidence that the stringent response inhibited GI of sigX/M.
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Affiliation(s)
- Mitsuo Ogura
- Institute of Oceanic Research and Development, Tokai University, 3-20-1 Orido, Shizuoka 424-8610, Japan
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