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Zhou Z, Li Z, Li Z. Exploring the molecular mechanisms of Lrp/AsnC-type transcription regulator DecR, an L-cysteine-responsive feast/famine regulatory protein. Int J Biol Macromol 2024; 270:132519. [PMID: 38768919 DOI: 10.1016/j.ijbiomac.2024.132519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
The Lrp/AsnC family of transcriptional regulators is commonly found in prokaryotes and is associated with the regulation of amino acid metabolism. However, it remains unclear how the L-cysteine-responsive Lrp/AsnC family regulator perceives and responds to L-cysteine. Here, we try to elucidate the molecular mechanism of the L-cysteine-responsive transcriptional regulator. Through 5'RACE and EMSA, we discovered a 15 bp incompletely complementary pair palindromic sequence essential for DecR binding, which differed slightly from the binding sequence of other Lrp/AsnC transcription regulators. Using alanine scanning, we identified the L-cysteine binding site on DecR and found that different Lrp/AsnC regulators adjust their binding pocket's side-chain residues to accommodate their specific effector. MD simulations were then conducted to explore how ligand binding influences the allosteric behavior of the protein. PCA and in silico docking revealed that ligand binding induced perturbations in the linker region, triggering conformational alterations and leading to the relocalization of the DNA-binding domains, enabling the embedding of the DNA-binding region of DecR into the DNA molecule, thereby enhancing DNA-binding affinity. Our findings can broaden the understanding of the recognition and regulatory mechanisms of the Lrp/AsnC-type transcription factors, providing a theoretical basis for further investigating the molecular mechanisms of other transcription factors.
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Affiliation(s)
- Zhiyou Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zonglin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China.
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2
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Feng Y, Jiang Y, Chen X, Zhu L, Xue H, Wu M, Yang L, Yu H, Lin J. Improving the production of carbamoyltobramycin by an industrial Streptoalloteichus tenebrarius through metabolic engineering. Appl Microbiol Biotechnol 2024; 108:304. [PMID: 38643456 PMCID: PMC11033246 DOI: 10.1007/s00253-024-13141-2] [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: 02/15/2024] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/22/2024]
Abstract
Tobramycin is an essential and extensively used broad-spectrum aminoglycoside antibiotic obtained through alkaline hydrolysis of carbamoyltobramycin, one of the fermentation products of Streptoalloteichus tenebrarius. To simplify the composition of fermentation products from industrial strain, the main byproduct apramycin was blocked by gene disruption and constructed a mutant mainly producing carbamoyltobramycin. The generation of antibiotics is significantly affected by the secondary metabolism of actinomycetes which could be controlled by modifying the pathway-specific regulatory proteins within the cluster. Within the tobramycin biosynthesis cluster, a transcriptional regulatory factor TobR belonging to the Lrp/AsnC family was identified. Based on the sequence and structural characteristics, tobR might encode a pathway-specific transcriptional regulatory factor during biosynthesis. Knockout and overexpression strains of tobR were constructed to investigate its role in carbamoyltobramycin production. Results showed that knockout of TobR increased carbamoyltobramycin biosynthesis by 22.35%, whereas its overexpression decreased carbamoyltobramycin production by 10.23%. In vitro electrophoretic mobility shift assay (EMSA) experiments confirmed that TobR interacts with DNA at the adjacent tobO promoter position. Strains overexpressing tobO with ermEp* promoter exhibited 36.36% increase, and tobO with kasOp* promoter exhibited 22.84% increase in carbamoyltobramycin titer. When the overexpressing of tobO and the knockout of tobR were combined, the production of carbamoyltobramycin was further enhanced. In the shake-flask fermentation, the titer reached 3.76 g/L, which was 42.42% higher than that of starting strain. Understanding the role of Lrp/AsnC family transcription regulators would be useful for other antibiotic biosynthesis in other actinomycetes. KEY POINTS: • The transcriptional regulator TobR belonging to the Lrp/AsnC family was identified. • An oxygenase TobO was identified within the tobramycin biosynthesis cluster. • TobO and TobR have significant effects on the synthesis of carbamoyltobramycin.
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Affiliation(s)
- Yun Feng
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Yiqi Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xutong Chen
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Li Zhu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Hailong Xue
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Mianbin Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Lirong Yang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China
| | - Haoran Yu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, China.
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China.
| | - Jianping Lin
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, China.
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Matarredona L, García-Bonete MJ, Guío J, Camacho M, Fillat MF, Esclapez J, Bonete MJ. Global Lrp regulator protein from Haloferax mediterranei: Transcriptional analysis and structural characterization. Int J Biol Macromol 2024; 260:129541. [PMID: 38244746 DOI: 10.1016/j.ijbiomac.2024.129541] [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: 11/24/2023] [Revised: 01/03/2024] [Accepted: 01/14/2024] [Indexed: 01/22/2024]
Abstract
Haloferax mediterranei, an extreme halophilic archaeon thriving in hypersaline environments, has acquired significant attention in biotechnological and biochemical research due to its remarkable ability to flourish in extreme salinity conditions. Transcription factors, essential in regulating diverse cellular processes, have become focal points in understanding its adaptability. This study delves into the role of the Lrp transcription factor, exploring its modulation of glnA, nasABC, and lrp gene promoters in vivo through β-galactosidase assays. Remarkably, our findings propose Lrp as the pioneering transcriptional regulator of nitrogen metabolism identified in a haloarchaeon. This study suggests its potential role in activating or repressing assimilatory pathway enzymes (GlnA and NasA). The interaction between Lrp and these promoters is analyzed using Electrophoretic Mobility Shift Assay and Differential Scanning Fluorimetry, highlighting l-glutamine's indispensable role in stabilizing the Lrp-DNA complex. Our research uncovers that halophilic Lrp forms octameric structures in the presence of l-glutamine. The study reveals the three-dimensional structure of the Lrp as a homodimer using X-ray crystallography, confirming this state in solution by Small-Angle X-ray Scattering. These findings illuminate the complex molecular mechanisms driving Hfx. mediterranei's nitrogen metabolism, offering valuable insights about its gene expression regulation and enriching our comprehension of extremophile biology.
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Affiliation(s)
- Laura Matarredona
- Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Grupo Biotecnología de Extremófilos, Universidad de Alicante, San Vicente del Raspeig, Alicante, Spain
| | - María-José García-Bonete
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine. University of Gothenburg, Sweden
| | - Jorge Guío
- Departamento de Bioquímica y Biología Molecular y Celular, Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - Mónica Camacho
- Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Grupo Biotecnología de Extremófilos, Universidad de Alicante, San Vicente del Raspeig, Alicante, Spain
| | - María F Fillat
- Departamento de Bioquímica y Biología Molecular y Celular, Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - Julia Esclapez
- Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Grupo Biotecnología de Extremófilos, Universidad de Alicante, San Vicente del Raspeig, Alicante, Spain.
| | - María-José Bonete
- Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Grupo Biotecnología de Extremófilos, Universidad de Alicante, San Vicente del Raspeig, Alicante, Spain.
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4
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Bernauw AJ, Crabbe V, Ryssegem F, Willaert R, Bervoets I, Peeters E. Molecular mechanisms of regulation by a β-alanine-responsive Lrp-type transcription factor from Acidianus hospitalis. Microbiologyopen 2023; 12:e1356. [PMID: 37379425 DOI: 10.1002/mbo3.1356] [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: 02/13/2023] [Revised: 04/22/2023] [Accepted: 04/30/2023] [Indexed: 06/30/2023] Open
Abstract
The leucine-responsive regulatory protein (Lrp) family of transcriptional regulators is widespread among prokaryotes and especially well-represented in archaea. It harbors members with diverse functional mechanisms and physiological roles, often linked to the regulation of amino acid metabolism. BarR is an Lrp-type regulator that is conserved in thermoacidophilic Thermoprotei belonging to the order Sulfolobales and is responsive to the non-proteinogenic amino acid β-alanine. In this work, we unravel molecular mechanisms of the Acidianus hospitalis BarR homolog, Ah-BarR. Using a heterologous reporter gene system in Escherichia coli, we demonstrate that Ah-BarR is a dual-function transcription regulator that is capable of repressing transcription of its own gene and activating transcription of an aminotransferase gene, which is divergently transcribed from a common intergenic region. Atomic force microscopy (AFM) visualization reveals a conformation in which the intergenic region appears wrapped around an octameric Ah-BarR protein. β-alanine causes small conformational changes without affecting the oligomeric state of the protein, resulting in a relief of regulation while the regulator remains bound to the DNA. This regulatory and ligand response is different from the orthologous regulators in Sulfolobus acidocaldarius and Sulfurisphaera tokodaii, which is possibly explained by a distinct binding site organization and/or by the presence of an additional C-terminal tail in Ah-BarR. By performing site-directed mutagenesis, this tail is shown to be involved in ligand-binding response.
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Affiliation(s)
- Amber J Bernauw
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Vincent Crabbe
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Fraukje Ryssegem
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ronnie Willaert
- Research Group Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Alliance Research Group VUB-UGent NanoMicrobiology, International Joint Research Group VUB-EFPL NanoBiotechnology & NanoMedicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Indra Bervoets
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Payá G, Bautista V, Camacho M, Esclapez J, Bonete MJ. Comprehensive Bioinformatics Analysis of the Biodiversity of Lsm Proteins in the Archaea Domain. Microorganisms 2023; 11:1196. [PMID: 37317170 DOI: 10.3390/microorganisms11051196] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq proteins. Sm and Lsm proteins are found in the Eukarya and Archaea domains, respectively, while Hfq proteins exist in the Bacteria domain. Even though Sm and Hfq proteins have been extensively studied, archaeal Lsm proteins still require further exploration. In this work, different bioinformatics tools are used to understand the diversity and distribution of 168 Lsm proteins in 109 archaeal species to increase the global understanding of these proteins. All 109 archaeal species analyzed encode one to three Lsm proteins in their genome. Lsm proteins can be classified into two groups based on molecular weight. Regarding the gene environment of lsm genes, many of these genes are located adjacent to transcriptional regulators of the Lrp/AsnC and MarR families, RNA-binding proteins, and ribosomal protein L37e. Notably, only proteins from species of the class Halobacteria conserved the internal and external residues of the RNA-binding site identified in Pyrococcus abyssi, despite belonging to different taxonomic orders. In most species, the Lsm genes show associations with 11 genes: rpl7ae, rpl37e, fusA, flpA, purF, rrp4, rrp41, hel308, rpoD, rpoH, and rpoN. We propose that most archaeal Lsm proteins are related to the RNA metabolism, and the larger Lsm proteins could perform different functions and/or act through other mechanisms of action.
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Affiliation(s)
- Gloria Payá
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Vanesa Bautista
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Mónica Camacho
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Julia Esclapez
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
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Liu J, Wang Y, He H, Dong S, Tang L, Yang E, Wang W, Zhang B. The leucine-responsive regulatory protein SCAB_Lrp modulates thaxtomin biosynthesis, pathogenicity, and morphological development in Streptomyces scabies. MOLECULAR PLANT PATHOLOGY 2023; 24:167-178. [PMID: 36478143 PMCID: PMC9831280 DOI: 10.1111/mpp.13285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/16/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Streptomyces scabies is the best-characterized plant-pathogenic streptomycete, which is a special species among the large genus Streptomyces. The pathogenicity of S. scabies relies on the production of the secondary metabolite thaxtomin A. Little is known about the molecular mechanisms underlying the regulation of thaxtomin biosynthesis in S. scabies beyond the pathway-specific activator TxtR and the cellulose utilization repressor CebR. The leucine-responsive regulatory protein (Lrp) family modulates secondary metabolism in nonpathogenic streptomycetes. However, the regulatory relationship between the Lrp and pathogenic streptomycetes remains unknown. In this study, we demonstrated that SCAB_Lrp (SCAB_77931) from S. scabies significantly affects thaxtomin biosynthesis, pathogenicity, and morphological development. SCAB_Lrp deletion resulted in a dramatic decline in thaxtomin A production and a low-virulence phenotype of S. scabies. An in-depth dissection of the regulatory mechanism of SCAB_Lrp revealed that it positively regulates the transcription of the thaxtomin biosynthetic gene cluster by directly binding to the promoter of the cluster-situated regulator gene txtR. SCAB_Lrp also controls the morphological development of S. scabies by directly activating the transcription of amfC, whiB, and ssgB. SCAB_Lrp directly controls the transcription of its own gene by binding a specific sequence (5'-GGACAGTCGCCGTGCTACG-3'). Moreover, phenylalanine and methionine have been characterized as SCAB_Lrp effectors by strengthening the binding affinity and complex status between SCAB_Lrp and DNA. Our findings characterize a multifunctional regulatory protein, SCAB_Lrp, that controls secondary metabolism, pathogenicity, and sporulation in S. scabies and provide new insights into the complex regulatory network that modulates thaxtomin phytotoxins in pathogenic Streptomyces.
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Affiliation(s)
- Jing Liu
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Yunxia Wang
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Haoyang He
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Shengnan Dong
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Lijuan Tang
- Institute of Physical Science and Information Technology, School of Life SciencesAnhui UniversityHefeiChina
| | - Endong Yang
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Weiyun Wang
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Buchang Zhang
- Institute of Physical Science and Information Technology, School of Life SciencesAnhui UniversityHefeiChina
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7
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Gagarinova A, Hosseinnia A, Rahmatbakhsh M, Istace Z, Phanse S, Moutaoufik MT, Zilocchi M, Zhang Q, Aoki H, Jessulat M, Kim S, Aly KA, Babu M. Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli. Nat Commun 2022; 13:4085. [PMID: 35835781 PMCID: PMC9283627 DOI: 10.1038/s41467-022-31819-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 07/05/2022] [Indexed: 11/25/2022] Open
Abstract
Bacterial transcription factors (TFs) are widely studied in Escherichia coli. Yet it remains unclear how individual genes in the underlying pathways of TF machinery operate together during environmental challenge. Here, we address this by applying an unbiased, quantitative synthetic genetic interaction (GI) approach to measure pairwise GIs among all TF genes in E. coli under auxotrophic (rich medium) and prototrophic (minimal medium) static growth conditions. The resulting static and differential GI networks reveal condition-dependent GIs, widespread changes among TF genes in metabolism, and new roles for uncharacterized TFs (yjdC, yneJ, ydiP) as regulators of cell division, putrescine utilization pathway, and cold shock adaptation. Pan-bacterial conservation suggests TF genes with GIs are co-conserved in evolution. Together, our results illuminate the global organization of E. coli TFs, and remodeling of genetic backup systems for TFs under environmental change, which is essential for controlling the bacterial transcriptional regulatory circuits. The bacterium E. coli has around 300 transcriptional factors, but the functions of many of them, and the interactions between their respective regulatory networks, are unclear. Here, the authors study genetic interactions among all transcription factor genes in E. coli, revealing condition-dependent interactions and roles for uncharacterized transcription factors.
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Affiliation(s)
- Alla Gagarinova
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Ali Hosseinnia
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | | | - Zoe Istace
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | | | - Mara Zilocchi
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Qingzhou Zhang
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Matthew Jessulat
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Sunyoung Kim
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Khaled A Aly
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada.
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Leucine-Responsive Regulatory Protein in Acetic Acid Bacteria Is Stable and Functions at a Wide Range of Intracellular pH Levels. J Bacteriol 2021; 203:e0016221. [PMID: 34228496 DOI: 10.1128/jb.00162-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acetic acid bacteria grow while producing acetic acid, resulting in acidification of the culture. Limited reports elucidate the effect of changes in intracellular pH on transcriptional factors. In the present study, the intracellular pH of Komagataeibacter europaeus was monitored with a pH-sensitive green fluorescent protein, showing that the intracellular pH decreased from 6.3 to 4.7 accompanied by acetic acid production during cell growth. The leucine-responsive regulatory protein of K. europaeus (KeLrp) was used as a model to examine pH-dependent effects, and its properties were compared with those of the Escherichia coli ortholog (EcLrp) at different pH levels. The DNA-binding activities of EcLrp and KeLrp with the target DNA (Ec-ilvI and Ke-ilvI) were examined by gel mobility shift assays under various pH conditions. EcLrp showed the highest affinity with the target at pH 8.0 (Kd [dissociation constant], 0.7 μM), decreasing to a minimum of 3.4 μM at pH 4.0. Conversely, KeLrp did not show significant differences in binding affinity between pH 4 and 7 (Kd, 1.0 to 1.5 μM), and the highest affinity was at pH 5.0 (Kd, 1.0 μM). Circular dichroism spectroscopy revealed that the α-helical content of KeLrp was the highest at pH 5.0 (49%) and was almost unchanged while being maintained at >45% over a range of pH levels examined, while that of EcLrp decreased from its maximum (49% at pH 7.0) to its minimum (36% at pH 4.0). These data indicate that KeLrp is stable and functions over a wide range of intracellular pH levels. IMPORTANCE Lrp is a highly conserved transcriptional regulator found in bacteria and archaea and regulates transcriptions of various genes. The intracellular pH of acetic acid bacteria (AAB) changes accompanied by acetic acid production during cell growth. The Lrp of AAB K. europaeus (KeLrp) was structurally stable over a wide range of pH and maintained DNA-binding activity even at low pH compared with Lrp from E. coli living in a neutral environment. An in vitro experiment showed DNA-binding activity of KeLrp to the target varied with changes in pH. In AAB, change of the intracellular pH during a cell growth would be an important trigger in controlling the activity of Lrp in vivo.
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Analysis of Haloferax mediterranei Lrp Transcriptional Regulator. Genes (Basel) 2021; 12:genes12060802. [PMID: 34070366 PMCID: PMC8229911 DOI: 10.3390/genes12060802] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022] Open
Abstract
Haloferax mediterranei is an extremely halophilic archaeon, able to live in hypersaline environments with versatile nutritional requirements, whose study represents an excellent basis in the field of biotechnology. The transcriptional machinery in Archaea combines the eukaryotic basal apparatus and the bacterial regulation mechanisms. However, little is known about molecular mechanisms of gene expression regulation compared with Bacteria, particularly in Haloarchaea. The genome of Hfx. mediterranei contains a gene, lrp (HFX_RS01210), which encodes a transcriptional factor belonging to Lrp/AsnC family. It is located downstream of the glutamine synthetase gene (HFX_RS01205), an enzyme involved in ammonium assimilation and amino acid metabolism. To study this transcriptional factor more deeply, the lrp gene has been homologously overexpressed and purified under native conditions by two chromatographic steps, namely nickel affinity and gel filtration chromatography, showing that Lrp behaves asa tetrameric protein of approximately 67 kDa. Its promoter region has been characterized under different growth conditions using bgaH as a reporter gene. The amount of Lrp protein was also analyzed by Western blotting in different nitrogen sources and under various stress conditions. To sum up, regarding its involvement in the nitrogen cycle, it has been shown that its expression profile does not change in response to the nitrogen sources tested. Differences in its expression pattern have been observed under different stress conditions, such as in the presence of hydrogen peroxide or heavy metals. According to these results, the Lrp seems to be involved in a general response against stress factors, acting as a first-line transcriptional regulator.
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Mariadasse R, Rajmichael R, Dwivedy A, Amala M, Ahmad M, Mutharasappan N, Biswal BK, Jeyakanthan J. Characterization of putative transcriptional regulator (PH0140) and its distal homologue. Cell Signal 2021; 84:110031. [PMID: 33932498 DOI: 10.1016/j.cellsig.2021.110031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/13/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022]
Abstract
In this study, a phylogenetic tree was constructed using 1854 sequences of various Lrp/AnsC (FFRPs) and ArsR proteins from pathogenic and non-pathogenic organisms. Despite having sequence similarities, FFRPs and ArsR proteins functioning differently as a transcriptional regulator and de-repressor in the presence of exogenous amino acids and metal ions, respectively. To understand these functional differences, the structures of various FFRPs and ArsR proteins (134 sequences) were modeled. Several ArsR proteins exhibited high similarity to the FFRPs while in few proteins, unusual structural folds were observed. However, the Helix-turn-Helix (HTH) domains are common among them and the ligand-binding domains are structurally dissimilar suggest the differences in their binding preferences. Despite low sequence conservation, most of these proteins revealed negatively charged surfaces in the active site pockets. Representative structures (PH0140 and TtArsR protein) from FFRPs and ArsR protein families were considered and evaluated for their functional differences using molecular modeling studies. Our earlier study has explained the binding preference of exogenous Tryptophan and the related transcriptional regulatory mechanism of PH0140 protein. In this study, a Cu2+ ion-induced de-repression mechanism of the TtArsR-DNA complex was characterized through docking and molecular dynamics. Further, the proteins were purified and their efficiency for sensing Tryptophan and Cu2+ ions were analyzed using cyclic voltammetry. Overall, the study explores the structural evolution and functional difference of FFRPs and ArsR proteins that present the possibilities of PH0140 and TtArsR as potential bio-sensory molecules.
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Affiliation(s)
- Richard Mariadasse
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India
| | - Raji Rajmichael
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India
| | | | - Mathimaran Amala
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India
| | | | - Nachiappan Mutharasappan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India
| | | | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India.
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Pastor-Soler S, Camacho M, Bautista V, Bonete MJ, Esclapez J. Towards the Elucidation of Assimilative nasABC Operon Transcriptional Regulation in Haloferax mediterranei. Genes (Basel) 2021; 12:genes12050619. [PMID: 33921943 PMCID: PMC8143581 DOI: 10.3390/genes12050619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/14/2021] [Accepted: 04/20/2021] [Indexed: 11/22/2022] Open
Abstract
The assimilatory pathway of the nitrogen cycle in the haloarchaeon Haloferax mediterranei has been well described and characterized in previous studies. However, the regulatory mechanisms involved in the gene expression of this pathway remain unknown in haloarchaea. This work focuses on elucidating the regulation at the transcriptional level of the assimilative nasABC operon (HFX_2002 to HFX_2004) through different approaches. Characterization of its promoter region using β-galactosidase as a reporter gene and site-directed mutagenesis has allowed us to identify possible candidate binding regions for a transcriptional factor. The identification of a potential transcriptional regulator related to nitrogen metabolism has become a real challenge due to the lack of information on haloarchaea. The investigation of protein–DNA binding by streptavidin bead pull-down analysis combined with mass spectrometry resulted in the in vitro identification of a transcriptional regulator belonging to the Lrp/AsnC family, which binds to the nasABC operon promoter (p.nasABC). To our knowledge, this study is the first report to suggest the AsnC transcriptional regulator as a powerful candidate to play a regulatory role in nasABC gene expression in Hfx. mediterranei and, in general, in the assimilatory nitrogen pathway.
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12
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Liu J, Li L, Wang Y, Li B, Cai X, Tang L, Dong S, Yang E, Wu H, Zhang B. Joint engineering of SACE_Lrp and its target MarR enhances the biosynthesis and export of erythromycin in Saccharopolyspora erythraea. Appl Microbiol Biotechnol 2021; 105:2911-2924. [PMID: 33760930 DOI: 10.1007/s00253-021-11228-8] [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: 12/21/2020] [Revised: 02/24/2021] [Accepted: 03/10/2021] [Indexed: 11/24/2022]
Abstract
The Lrp and MarR families are two groups of transcriptional regulators widely distributed among prokaryotes. However, the hierarchical-regulatory relationship between the Lrp family and the MarR family remains unknown. Our previous study found that an Lrp (SACE_Lrp) from Saccharopolyspora erythraea indirectly repressed the biosynthesis of erythromycin. In this study, we characterized a novel MarR family protein (SACE_6745) from S. erythraea, which is controlled by SACE_Lrp and plays a direct regulatory role in erythromycin biosynthesis and export. SACE_Lrp directly regulated the expression of marR by specifically binding a precise site OM (5'-CTCCGGGAACCATT-3'). Gene disruption of marR increased the production of erythromycin by 45% in S. erythraea A226. We found that MarR has direct DNA-binding activity for the promoter regions of the erythromycin biosynthetic genes, as well as an ABC exporter SACE_2701-2702 which was genetically proved to be responsible for erythromycin efflux. Disruption of SACE_Lrp in industrial S. erythraea WB was an efficient strategy to enhance erythromycin production. Herein, we jointly engineered SACE_Lrp and its target MarR by deleting marR in WBΔSACE_Lrp, resulting in 20% increase in erythromycin yield in mutant WBΔLrpΔmarR compared to WBΔSACE_Lrp, and 39% to WB. Overall, our findings provide new insights into the hierarchical-regulatory relationship of Lrp and MarR proteins and new avenues for coordinating antibiotic biosynthesis and export by joint engineering regulators in actinomycetes. KEY POINTS: • The hierarchical-regulatory relationship between SACE_Lrp and MarR was identified. • MarR directly controlled the expression of erythromycin biosynthesis and export genes. • Joint engineering of SACE_Lrp-MarR regulatory element enhanced erythromycin production.
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Affiliation(s)
- Jing Liu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| | - Long Li
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yunxia Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Bowen Li
- Institute of Physical Science and Information Technology, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Xinlu Cai
- Institute of Physical Science and Information Technology, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Lijuan Tang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Shengnan Dong
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Endong Yang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hang Wu
- Institute of Physical Science and Information Technology, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Buchang Zhang
- Institute of Physical Science and Information Technology, School of Life Sciences, Anhui University, Hefei, 230601, China.
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13
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Faucher C, Mazana V, Kardacz M, Parthuisot N, Ferdy JB, Duneau D. Step-Specific Adaptation and Trade-Off over the Course of an Infection by GASP Mutation Small Colony Variants. mBio 2021; 12:e01399-20. [PMID: 33436427 PMCID: PMC7845629 DOI: 10.1128/mbio.01399-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/17/2020] [Indexed: 11/20/2022] Open
Abstract
During an infection, parasites face a succession of challenges, each decisive for disease outcome. The diversity of challenges requires a series of parasite adaptations to successfully multiply and transmit from host to host. Thus, the pathogen genotypes that succeed during one step might be counterselected in later stages of the infection. Using the bacterium Xenorhabdus nematophila and adult Drosophila melanogaster flies as hosts, we showed that such step-specific adaptations, here linked to GASP (i.e., growth advantage in stationary phase) mutations in the X. nematophila master gene regulator lrp, exist and can trade off with each other. We found that nonsense lrp mutations had lowered the ability to resist the host immune response, while all classes of mutations in lrp were associated with a decrease in the ability to proliferate during early infection. We demonstrate that reduced proliferation of X. nematophila best explains diminished virulence in this infection model. Finally, decreased proliferation during the first step of infection is accompanied by improved proliferation during late infection, suggesting a trade-off between the adaptations to each step. Step-specific adaptations could play a crucial role in the chronic phase of infections in any disease organisms that show similar small colony variants (SCVs) to X. nematophilaIMPORTANCE Within-host evolution has been described in many bacterial diseases, and the genetic basis behind the adaptations has stimulated a lot of interest. Yet, the studied adaptations are generally focused on antibiotic resistance and rarely on the adaptation to the environment given by the host, and the potential trade-offs hindering adaptations to each step of the infection are rarely considered. Those trade-offs are key to understanding intrahost evolution and thus the dynamics of the infection. However, understanding these trade-offs supposes a detailed study of host-pathogen interactions at each step of the infection process, with an adapted methodology for each step. Using Drosophila melanogaster as the host and the bacterium Xenorhabdus nematophila, we investigated the bacterial adaptations resulting from GASP mutations known to induce the small colony variant (SCV) phenotype positively selected within the host over the course of an infection, as well as the trade-off between step-specific adaptations.
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Affiliation(s)
- Christian Faucher
- CNRS, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Vincent Mazana
- CNRS, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Marion Kardacz
- CNRS, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Nathalie Parthuisot
- CNRS, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Jean-Baptiste Ferdy
- CNRS, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - David Duneau
- CNRS, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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14
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Grünberger F, Reichelt R, Waege I, Ned V, Bronner K, Kaljanac M, Weber N, El Ahmad Z, Knauss L, Madej MG, Ziegler C, Grohmann D, Hausner W. CopR, a Global Regulator of Transcription to Maintain Copper Homeostasis in Pyrococcus furiosus. Front Microbiol 2021; 11:613532. [PMID: 33505379 PMCID: PMC7830388 DOI: 10.3389/fmicb.2020.613532] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/09/2020] [Indexed: 11/24/2022] Open
Abstract
Although copper is in many cases an essential micronutrient for cellular life, higher concentrations are toxic. Therefore, all living cells have developed strategies to maintain copper homeostasis. In this manuscript, we have analyzed the transcriptome-wide response of Pyrococcus furiosus to increased copper concentrations and described the essential role of the putative copper-sensing metalloregulator CopR in the detoxification process. To this end, we employed biochemical and biophysical methods to characterize the role of CopR. Additionally, a copR knockout strain revealed an amplified sensitivity in comparison to the parental strain towards increased copper levels, which designates an essential role of CopR for copper homeostasis. To learn more about the CopR-regulated gene network, we performed differential gene expression and ChIP-seq analysis under normal and 20 μM copper-shock conditions. By integrating the transcriptome and genome-wide binding data, we found that CopR binds to the upstream regions of many copper-induced genes. Negative-stain transmission electron microscopy and 2D class averaging revealed an octameric assembly formed from a tetramer of dimers for CopR, similar to published crystal structures from the Lrp family. In conclusion, we propose a model for CopR-regulated transcription and highlight the regulatory network that enables Pyrococcus to respond to increased copper concentrations.
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Affiliation(s)
- Felix Grünberger
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Robert Reichelt
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Ingrid Waege
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Verena Ned
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Korbinian Bronner
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Marcell Kaljanac
- Department of Structural Biology, Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Nina Weber
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Zubeir El Ahmad
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Lena Knauss
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - M. Gregor Madej
- Department of Structural Biology, Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Christine Ziegler
- Department of Structural Biology, Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Winfried Hausner
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
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15
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Sivakumar R, Gunasekaran P, Rajendhran J. Functional characterization of asnC family transcriptional regulator in Pseudomonas aeruginosa PGPR2 during root colonization. Mol Biol Rep 2020; 47:7941-7957. [PMID: 33011891 DOI: 10.1007/s11033-020-05872-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022]
Abstract
Transcriptional regulators in bacteria are the crucial players in mediating communication between environmental cues and DNA transcription through a complex network process. Pseudomonas aeruginosa PGPR2 is an efficient root colonizer and a biocontrol strain. Previously, we identified that the transcriptional regulator, asnC, negatively regulates the corn root colonization of P. aeruginosa PGPR2. In a transposon insertion sequencing (INSeq) screen, the asnC insertion mutant was positively selected during root colonization, meaning the disruption of asnC improves the fitness of the P. aeruginosa PGPR2 strain for the root colonization. In this study, we constructed isogenic mutant of asnC family transcriptional regulator encoded by PGPR2_17510 by allele exchange mutagenesis. The ΔasnC mutant was able to efficiently colonize corn roots with a twofold increase in population when compared to the wild-type strain. Similarly, the mutant strain outcompeted the wild-type strain in a competition assay, where the mutant strain represented 90% of the total population recovered from the root. We compared the whole transcriptome of the wild-type and the ΔasnC mutant of P. aeruginosa PGPR2 when exposed to the corn root exudates. The RNA-Seq revealed that a total of 360 genes were differentially expressed in the ΔasnC strain of P. aeruginosa PGPR2. Inactivation of asnC transcriptional regulator resulted in the up-regulation of several genetic factors implicated in metabolism, uptake of nutrients, motility, stress response, and signal transduction, which could play crucial roles in root colonization. This notion was further validated by phenotypic characterization and quantification of transcription pattern of selected genes associated with metabolism, motility, and carbon catabolite repression between wild type and mutant strain, which was in agreement with transcriptome data. Similarly, ΔasnC strain formed increased biofilm on abiotic surface validating our RNA-seq analysis, where transcript levels of several genes associated with biofilm formation were up-regulated in the mutant strain. We report that the inactivation of an asnC family transcriptional regulator encoded by PGPR2_17510 enhances the root colonization and biofilm-forming ability of P. aeruginosa PGPR2. Together, our results provide evidence for the molecular adaptations that enable ΔasnC mutant strain to colonize on the corn roots and to form a biofilm.
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Affiliation(s)
- Ramamoorthy Sivakumar
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India
| | | | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India.
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16
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Rodríguez-Herrero V, Payá G, Bautista V, Vegara A, Cortés-Molina M, Camacho M, Esclapez J, Bonete MJ. Essentiality of the glnA gene in Haloferax mediterranei: gene conversion and transcriptional analysis. Extremophiles 2020; 24:433-446. [PMID: 32296946 DOI: 10.1007/s00792-020-01169-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/27/2020] [Indexed: 11/26/2022]
Abstract
Glutamine synthetase is an essential enzyme in ammonium assimilation and glutamine biosynthesis. The Haloferax mediterranei genome has two other glnA-type genes (glnA2 and glnA3) in addition to the glutamine synthetase gene glnA. To determine whether the glnA2 and glnA3 genes can replace glnA in nitrogen metabolism, we generated deletion mutants of glnA. The glnA deletion mutants could not be generated in a medium without glutamine, and thus, glnA is an essential gene in H. mediterranei. The glnA deletion mutant was achieved by adding 40 mM glutamine to the selective medium. This conditional HM26-ΔglnA mutant was characterised with different approaches in the presence of distinct nitrogen sources and nitrogen starvation. Transcriptomic analysis was performed to compare the expression profiles of the strains HM26-ΔglnA and HM26 under different growth conditions. The glnA deletion did not affect the expression of glnA2, glnA3 and nitrogen assimilation genes under nitrogen starvation. Moreover, the results showed that glnA, glnA2 and glnA3 were not expressed under the same conditions. These results indicated that glnA is an essential gene for H. mediterranei and, therefore, glnA2 and glnA3 cannot replace glnA in the conditions analysed.
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Affiliation(s)
- V Rodríguez-Herrero
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - G Payá
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - V Bautista
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - A Vegara
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - M Cortés-Molina
- Departamento de Matemática Aplicada, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - M Camacho
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - J Esclapez
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - M J Bonete
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain.
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17
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Xu Y, Tang Y, Wang N, Liu J, Cai X, Cai H, Li J, Tan G, Liu R, Bai L, Zhang L, Wu H, Zhang B. Transcriptional regulation of a leucine-responsive regulatory protein for directly controlling lincomycin biosynthesis in Streptomyces lincolnensis. Appl Microbiol Biotechnol 2020; 104:2575-2587. [DOI: 10.1007/s00253-020-10381-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/06/2020] [Accepted: 01/16/2020] [Indexed: 12/19/2022]
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18
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Sanchez I, Hernandez-Guerrero R, Mendez-Monroy PE, Martinez-Nuñez MA, Ibarra JA, Pérez-Rueda E. Evaluation of the Abundance of DNA-Binding Transcription Factors in Prokaryotes. Genes (Basel) 2020; 11:genes11010052. [PMID: 31947717 PMCID: PMC7017128 DOI: 10.3390/genes11010052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/13/2019] [Accepted: 12/25/2019] [Indexed: 02/03/2023] Open
Abstract
The ability of bacteria and archaea to modulate metabolic process, defensive response, and pathogenic capabilities depend on their repertoire of genes and capacity to regulate the expression of them. Transcription factors (TFs) have fundamental roles in controlling these processes. TFs are proteins dedicated to favor and/or impede the activity of the RNA polymerase. In prokaryotes these proteins have been grouped into families that can be found in most of the different taxonomic divisions. In this work, the association between the expansion patterns of 111 protein regulatory families was systematically evaluated in 1351 non-redundant prokaryotic genomes. This analysis provides insights into the functional and evolutionary constraints imposed on different classes of regulatory factors in bacterial and archaeal organisms. Based on their distribution, we found a relationship between the contents of some TF families and genome size. For example, nine TF families that represent 43.7% of the complete collection of TFs are closely associated with genome size; i.e., in large genomes, members of these families are also abundant, but when a genome is small, such TF family sizes are decreased. In contrast, almost 102 families (56.3% of the collection) do not exhibit or show only a low correlation with the genome size, suggesting that a large proportion of duplication or gene loss events occur independently of the genome size and that various yet-unexplored questions about the evolution of these TF families remain. In addition, we identified a group of families that have a similar distribution pattern across Bacteria and Archaea, suggesting common functional and probable coevolution processes, and a group of families universally distributed among all the genomes. Finally, a specific association between the TF families and their additional domains was identified, suggesting that the families sense specific signals or make specific protein-protein contacts to achieve the regulatory roles.
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Affiliation(s)
- Israel Sanchez
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida.C.P. 97302, Yucatán, Mexico; (I.S.); (R.H.-G.); (P.E.M.-M.)
| | - Rafael Hernandez-Guerrero
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida.C.P. 97302, Yucatán, Mexico; (I.S.); (R.H.-G.); (P.E.M.-M.)
| | - Paul Erick Mendez-Monroy
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida.C.P. 97302, Yucatán, Mexico; (I.S.); (R.H.-G.); (P.E.M.-M.)
| | - Mario Alberto Martinez-Nuñez
- Unidad Académica de Ciencias y Tecnología de Yucatán, UMDI-Sisal. Facultad de Ciencias, UNAM, Mérida C.P. 97302, Yucatán, Mexico;
| | - Jose Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México C.P. 11340, Mexico;
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida.C.P. 97302, Yucatán, Mexico; (I.S.); (R.H.-G.); (P.E.M.-M.)
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago C.P. 7500000, Chile
- Correspondence: ; Tel.: +52-9994060003 (ext. 7610)
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19
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Mariadasse R, Choubey SK, Jeyakanthan J. Insights into Exogenous Tryptophan-Mediated Allosteric Communication and Helical Transition of TRP Protein for Transcription Regulation. J Chem Inf Model 2019; 60:175-191. [DOI: 10.1021/acs.jcim.9b00755] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Richard Mariadasse
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004 Tamil Nadu, India
| | - Sanjay Kumar Choubey
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004 Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004 Tamil Nadu, India
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20
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Kim SY, Jeong HJ, Kim M, Choi AR, Kim MS, Kang SG, Lee SJ. Characterization of the copper-sensing transcriptional regulator CopR from the hyperthermophilic archeaon Thermococcus onnurineus NA1. Biometals 2019; 32:923-937. [PMID: 31676935 DOI: 10.1007/s10534-019-00223-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/28/2019] [Indexed: 12/28/2022]
Abstract
A putative copper ion-sensing transcriptional regulator CopR (TON_0836) from Thermococcus onnurineus NA1 was characterized. The CopR protein consists of a winged helix-turn-helix DNA-binding domain in the amino-terminal region and a TRASH domain that is assumed to be involved in metal ion-sensing in the carboxyl-terminal region. The CopR protein was most strongly bound to a region between its own gene promoter and a counter directional promoter region for copper efflux system CopA. When the divalent metals such as nickel, cobalt, copper, and iron were present, the CopR protein was dissociated from the target promoters on electrophoretic mobility shift assay (EMSA). The highest sensible ion is copper which affected protein releasing under 10 µM concentrations. CopR recognizes a significant upstream region of TATA box on CopR own promoter and acts as a transcriptional repressor in an in vitro transcription assay. Through site-directed mutagenesis of the DNA-binding domain, R34M mutant protein completely lost the DNA-binding activity on target promoter. When the conserved cysteine residues in C144XXC147 motif 1 of the TRASH domain were mutated into glycine, the double cysteine residue mutant protein alone lost the copper-binding activity. Therefore, CopR is a copper-sensing transcriptional regulator and acts as a repressor for autoregulation and for a putative copper efflux system CopA of T. onnurineus NA1.
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Affiliation(s)
- Seo-Yeon Kim
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, South Korea.,Educational Administration of Gyonggido, Euijungbu, 11759, South Korea
| | - Hong Joo Jeong
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, South Korea.,ImmuneMed, College of Medicine, Hallym University, Chuncheon, 24252, South Korea
| | - Minwook Kim
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, South Korea.,Department of Developmental Biology, Pittsburgh Liver Research Center, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Ae Ran Choi
- Marine Biotechnology Research Center, Marine Resources Research Division, Korea Institute of Ocean Science and Technology, Busan, 49111, South Korea
| | - Min-Sik Kim
- Marine Biotechnology Research Center, Marine Resources Research Division, Korea Institute of Ocean Science and Technology, Busan, 49111, South Korea.,Korea Institute of Energy Research, Daejon, 34129, South Korea
| | - Sung Gyun Kang
- Marine Biotechnology Research Center, Marine Resources Research Division, Korea Institute of Ocean Science and Technology, Busan, 49111, South Korea
| | - Sung-Jae Lee
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, South Korea.
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21
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Chen KY, Rathod J, Chiu YC, Chen JW, Tsai PJ, Huang IH. The Transcriptional Regulator Lrp Contributes to Toxin Expression, Sporulation, and Swimming Motility in Clostridium difficile. Front Cell Infect Microbiol 2019; 9:356. [PMID: 31681632 PMCID: PMC6811523 DOI: 10.3389/fcimb.2019.00356] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/02/2019] [Indexed: 12/17/2022] Open
Abstract
Clostridium difficile is a Gram-positive, spore-forming bacterium, and major cause of nosocomial diarrhea. Related studies have identified numerous factors that influence virulence traits such as the production of the two primary toxins, toxin A (TcdA) and toxin B (TcdB), as well as sporulation, motility, and biofilm formation. However, multiple putative transcriptional regulators are reportedly encoded in the genome, and additional factors are likely involved in virulence regulation. Although the leucine-responsive regulatory protein (Lrp) has been studied extensively in Gram-negative bacteria, little is known about its function in Gram-positive bacteria, although homologs have been identified in the genome. This study revealed that disruption of the lone lrp homolog in C. difficile decelerated growth under nutrient-limiting conditions, increased TcdA and TcdB production. Lrp was also found to negatively regulate sporulation while positively regulate swimming motility in strain R20291, but not in strain 630. The C. difficile Lrp appeared to function through transcriptional repression or activation. In addition, the lrp mutant was relatively virulent in a mouse model of infection. The results of this study collectively demonstrated that Lrp has broad regulatory function in C. difficile toxin expression, sporulation, motility, and pathogenesis.
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Affiliation(s)
- Kuan-Yu Chen
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jagat Rathod
- Department of Earth Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Ching Chiu
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jenn-Wei Chen
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Jane Tsai
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan.,Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - I-Hsiu Huang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
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22
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Sanders TJ, Marshall CJ, Santangelo TJ. The Role of Archaeal Chromatin in Transcription. J Mol Biol 2019; 431:4103-4115. [PMID: 31082442 PMCID: PMC6842674 DOI: 10.1016/j.jmb.2019.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/02/2019] [Accepted: 05/04/2019] [Indexed: 02/08/2023]
Abstract
Genomic organization impacts accessibility and movement of information processing systems along DNA. DNA-bound proteins dynamically dictate gene expression and provide regulatory potential to tune transcription rates to match ever-changing environmental conditions. Archaeal genomes are typically small, circular, gene dense, and organized either by histone proteins that are homologous to their eukaryotic counterparts, or small basic proteins that function analogously to bacterial nucleoid proteins. We review here how archaeal genomes are organized and how such organization impacts archaeal gene expression, focusing on conserved DNA-binding proteins within the clade and the factors that are known to impact transcription initiation and elongation within protein-bound genomes.
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Affiliation(s)
- Travis J Sanders
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Craig J Marshall
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
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23
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Transcription Regulators in Archaea: Homologies and Differences with Bacterial Regulators. J Mol Biol 2019; 431:4132-4146. [DOI: 10.1016/j.jmb.2019.05.045] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/08/2019] [Accepted: 05/24/2019] [Indexed: 11/17/2022]
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24
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Bervoets I, Charlier D. Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology. FEMS Microbiol Rev 2019; 43:304-339. [PMID: 30721976 PMCID: PMC6524683 DOI: 10.1093/femsre/fuz001] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
Gene expression occurs in two essential steps: transcription and translation. In bacteria, the two processes are tightly coupled in time and space, and highly regulated. Tight regulation of gene expression is crucial. It limits wasteful consumption of resources and energy, prevents accumulation of potentially growth inhibiting reaction intermediates, and sustains the fitness and potential virulence of the organism in a fluctuating, competitive and frequently stressful environment. Since the onset of studies on regulation of enzyme synthesis, numerous distinct regulatory mechanisms modulating transcription and/or translation have been discovered. Mostly, various regulatory mechanisms operating at different levels in the flow of genetic information are used in combination to control and modulate the expression of a single gene or operon. Here, we provide an extensive overview of the very diverse and versatile bacterial gene regulatory mechanisms with major emphasis on their combined occurrence, intricate intertwinement and versatility. Furthermore, we discuss the potential of well-characterized basal expression and regulatory elements in synthetic biology applications, where they may ensure orthogonal, predictable and tunable expression of (heterologous) target genes and pathways, aiming at a minimal burden for the host.
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Affiliation(s)
- Indra Bervoets
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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25
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Characterization and engineering of the Lrp/AsnC family regulator SACE_5717 for erythromycin overproduction in Saccharopolyspora erythraea. J Ind Microbiol Biotechnol 2019; 46:1013-1024. [PMID: 31016583 DOI: 10.1007/s10295-019-02178-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/04/2019] [Indexed: 10/27/2022]
Abstract
In this work, we found that the Lrp/AsnC family protein SACE_5717 negatively regulated erythromycin biosynthesis in S. erythraea. Disruption of SACE_5717 led to a 27% improvement in the yield of erythromycin in S. erythraea A226. SACE_5717 directly repressed its own gene expression, as well as that of the adjacent gene SACE_5716 by binding to the target sequence 5'-GAACGTTCGCCGTCACGCC-3'. The predicted LysE superfamily protein SACE_5716 directly influenced the export of lysine, histidine, threonine and glycine in S. erythraea. Arginine, tyrosine and tryptophan were characterized as the effectors of SACE_5717 by weakening the binding affinity of SACE_5717. In the industrial S. erythraea WB strain, deletion of SACE_5717 (WBΔSACE_5717) increased erythromycin yield by 20%, and by 36% when SACE_5716 was overexpressed in WBΔSACE_5717 (WBΔSACE_5717/5716). In large-scale 5-L fermentation experiment, erythromycin yield in the engineered strain WBΔSACE_5717/5716 reached 4686 mg/L, a 41% enhancement over 3323 mg/L of the parent WB strain.
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26
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Bischof LF, Haurat MF, Albers SV. Two membrane-bound transcription factors regulate expression of various type-IV-pili surface structures in Sulfolobus acidocaldarius. PeerJ 2019; 7:e6459. [PMID: 30828487 PMCID: PMC6396743 DOI: 10.7717/peerj.6459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/15/2019] [Indexed: 11/20/2022] Open
Abstract
In Archaea and Bacteria, gene expression is tightly regulated in response to environmental stimuli. In the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius nutrient limitation induces expression of the archaellum, the archaeal motility structure. This expression is orchestrated by a complex hierarchical network of positive and negative regulators-the archaellum regulatory network (arn). The membrane-bound one-component system ArnR and its paralog ArnR1 were recently described as main activators of archaellum expression in S. acidocaldarius. They regulate gene expression of the archaellum operon by targeting the promoter of flaB, encoding the archaellum filament protein. Here we describe a strategy for the isolation and biochemical characterization of these two archaellum regulators. Both regulators are capable of forming oligomers and are phosphorylated by the Ser/Thr kinase ArnC. Apart from binding to pflaB, ArnR but not ArnR1 bound to promoter sequences of aapF and upsX, which encode components of the archaeal adhesive pilus and UV-inducible pili system, demonstrating a regulatory connection between different surface appendages of S. acidocaldarius.
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Affiliation(s)
- Lisa Franziska Bischof
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Freiburg, Germany
| | - Maria Florencia Haurat
- Department of Molecular Microbiology, Washington University, School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sonja-Verena Albers
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
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27
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Lu Z, Zhang X, Dai J, Wang Y, He W. Engineering of leucine-responsive regulatory protein improves spiramycin and bitespiramycin biosynthesis. Microb Cell Fact 2019; 18:38. [PMID: 30782164 PMCID: PMC6379999 DOI: 10.1186/s12934-019-1086-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/07/2019] [Indexed: 11/21/2022] Open
Abstract
Background Bitespiramycin (BT) is produced by recombinant spiramycin (SP) producing strain Streptomyces spiramyceticus harboring a heterologous 4″-O-isovaleryltransferase gene (ist). Exogenous l-Leucine (l-Leu) could improve the production of BT. The orf2 gene found from the genomic sequence of S. spiramyceticus encodes a leucine-responsive regulatory protein (Lrp) family regulator named as SSP_Lrp. The functions of SSP_Lrp and l-Leu involved in the biosynthesis of spiramycin (SP) and BT were investigated in S. spiramyceticus. Results SSP_Lrp was a global regulator directly affecting the expression of three positive regulatory genes, bsm23, bsm42 and acyB2, in SP or BT biosynthesis. Inactivation of SSP_Lrp gene in S. spiramyceticus 1941 caused minor increase of SP production. However, SP production of the ΔSSP_Lrp-SP strain containing an SSP_Lrp deficient of putative l-Leu binding domain was higher than that of S. spiramyceticus 1941 (476.2 ± 3.1 μg/L versus 313.3 ± 25.2 μg/L, respectively), especially SP III increased remarkably. The yield of BT in ΔSSP_Lrp-BT strain was more than twice than that in 1941-BT. The fact that intracellular concentrations of branched-chain amino acids (BCAAs) decreased markedly in the ΔSSP_Lrp-SP demonstrated increasing catabolism of BCAAs provided more precursors for SP biosynthesis. Comparative analysis of transcriptome profiles of the ΔSSP_Lrp-SP and S. spiramyceticus 1941 found 12 genes with obvious differences in expression, including 6 up-regulated genes and 6 down-regulated genes. The up-regulated genes are related to PKS gene for SP biosynthesis, isoprenoid biosynthesis, a Sigma24 family factor, the metabolism of aspartic acid, pyruvate and acyl-CoA; and the down-regulated genes are associated with ribosomal proteins, an AcrR family regulator, and biosynthesis of terpenoid, glutamate and glutamine. Conclusion SSP_Lrp in S. spiramyceticus was a negative regulator involved in the SP and BT biosynthesis. The deletion of SSP_Lrp putative l-Leu binding domain was advantageous for production of BT and SP, especially their III components. Electronic supplementary material The online version of this article (10.1186/s12934-019-1086-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhili Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xiaoting Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, No. 1 Tian Tan Xi Li, Beijing, 100050, People's Republic of China
| | - Jianlu Dai
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, No. 1 Tian Tan Xi Li, Beijing, 100050, People's Republic of China
| | - Yiguang Wang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, No. 1 Tian Tan Xi Li, Beijing, 100050, People's Republic of China
| | - Weiqing He
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, No. 1 Tian Tan Xi Li, Beijing, 100050, People's Republic of China.
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28
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Bischof LF, Haurat MF, Hoffmann L, Albersmeier A, Wolf J, Neu A, Pham TK, Albaum SP, Jakobi T, Schouten S, Neumann-Schaal M, Wright PC, Kalinowski J, Siebers B, Albers SV. Early Response of Sulfolobus acidocaldarius to Nutrient Limitation. Front Microbiol 2019; 9:3201. [PMID: 30687244 PMCID: PMC6335949 DOI: 10.3389/fmicb.2018.03201] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/10/2018] [Indexed: 01/13/2023] Open
Abstract
In natural environments microorganisms encounter extreme changes in temperature, pH, osmolarities and nutrient availability. The stress response of many bacterial species has been described in detail, however, knowledge in Archaea is limited. Here, we describe the cellular response triggered by nutrient limitation in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. We measured changes in gene transcription and protein abundance upon nutrient depletion up to 4 h after initiation of nutrient depletion. Transcript levels of 1118 of 2223 protein coding genes and abundance of approximately 500 proteins with functions in almost all cellular processes were affected by nutrient depletion. Our study reveals a significant rerouting of the metabolism with respect to degradation of internal as well as extracellular-bound organic carbon and degradation of proteins. Moreover, changes in membrane lipid composition were observed in order to access alternative sources of energy and to maintain pH homeostasis. At transcript level, the cellular response to nutrient depletion in S. acidocaldarius seems to be controlled by the general transcription factors TFB2 and TFEβ. In addition, ribosome biogenesis is reduced, while an increased protein degradation is accompanied with a loss of protein quality control. This study provides first insights into the early cellular response of Sulfolobus to organic carbon and organic nitrogen depletion.
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Affiliation(s)
- Lisa F Bischof
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - M Florencia Haurat
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Lena Hoffmann
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Andreas Albersmeier
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jacqueline Wolf
- Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
| | - Astrid Neu
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Trong Khoa Pham
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
| | - Stefan P Albaum
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Jakobi
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Stefan Schouten
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute of Sea Research, Den Burg, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
| | - Phillip C Wright
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
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29
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Enhancement of precursor amino acid supplies for improving bacitracin production by activation of branched chain amino acid transporter BrnQ and deletion of its regulator gene lrp in Bacillus licheniformis. Synth Syst Biotechnol 2018; 3:236-243. [PMID: 30417137 PMCID: PMC6215969 DOI: 10.1016/j.synbio.2018.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/07/2018] [Accepted: 10/24/2018] [Indexed: 11/21/2022] Open
Abstract
Bacitracin, a new type of cyclic peptide antibiotic, is widely used as the feed additive in feed industry. Branched chain amino acids (BCAAs) are the key precursors for bacitracin synthesis. In this research, soybean meal was served as the raw material to supply precursor amino acids for bacitracin synthesis, and enhanced production of bacitracin was attempted by engineering BCAA transporter BrnQ and its regulator Lrp in the bacitracin industrial production strain Bacillus licheniformis DW2. Firstly, our results confirmed that Lrp negatively affected bacitracin synthesis in DW2, and deletion of lrp improved intracellular BCAA accumulations, as well as the expression level of BCAA transporter BrnQ, which further led to a 14.71% increase of bacitracin yield, compared with that of DW2. On the contrary, overexpression of Lrp decreased bacitracin yield by 12.28%. Secondly, it was suggested that BrnQ acted as a BCAA importer in DW2, and overexpression of BrnQ enhanced the intracellular BCAA accumulations and 10.43% of bacitracin yield. While, the bacitracin yield decreased by 18.27% in the brnQ deletion strain DW2△brnQ. Finally, BrnQ was further overexpressed in lrp deletion strain DW2△lrp, and bacitracin yield produced by the final strain DW2△lrp::BrnQ was 965.34 U/mL, increased by 22.42% compared with that of DW2 (788.48 U/mL). Collectively, this research confirmed that Lrp affected bacitracin synthesis via regulating the expression of BCAA transporter BrnQ and BCAA distributions, and provided a promising strain for industrial production of bacitracin.
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30
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Plominsky AM, Henríquez-Castillo C, Delherbe N, Podell S, Ramirez-Flandes S, Ugalde JA, Santibañez JF, van den Engh G, Hanselmann K, Ulloa O, De la Iglesia R, Allen EE, Trefault N. Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation. Front Microbiol 2018; 9:1800. [PMID: 30154761 PMCID: PMC6102401 DOI: 10.3389/fmicb.2018.01800] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 07/17/2018] [Indexed: 11/23/2022] Open
Abstract
Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cáhuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cáhuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cáhuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them.
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Affiliation(s)
- Alvaro M Plominsky
- Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía, Concepción, Chile
| | - Carlos Henríquez-Castillo
- Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía, Concepción, Chile
| | - Nathalie Delherbe
- Biology Department, Cell and Molecular Biology Joint Doctoral Program with UC San Diego, San Diego State University, San Diego, CA, United States
| | - Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Salvador Ramirez-Flandes
- Instituto Milenio de Oceanografía, Concepción, Chile.,Programa de Doctorado en Ingeniería de Sistemas Complejos, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Juan A Ugalde
- uBiome, Inc., San Francisco, CA, United States.,Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Juan F Santibañez
- Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, Concepción, Chile
| | | | - Kurt Hanselmann
- Department of Earth Sciences, ETH Zürich, Zurich, Switzerland
| | - Osvaldo Ulloa
- Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía, Concepción, Chile
| | - Rodrigo De la Iglesia
- Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
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31
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Martinez-Pastor M, Tonner PD, Darnell CL, Schmid AK. Transcriptional Regulation in Archaea: From Individual Genes to Global Regulatory Networks. Annu Rev Genet 2018; 51:143-170. [PMID: 29178818 DOI: 10.1146/annurev-genet-120116-023413] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Archaea are major contributors to biogeochemical cycles, possess unique metabolic capabilities, and resist extreme stress. To regulate the expression of genes encoding these unique programs, archaeal cells use gene regulatory networks (GRNs) composed of transcription factor proteins and their target genes. Recent developments in genetics, genomics, and computational methods used with archaeal model organisms have enabled the mapping and prediction of global GRN structures. Experimental tests of these predictions have revealed the dynamical function of GRNs in response to environmental variation. Here, we review recent progress made in this area, from investigating the mechanisms of transcriptional regulation of individual genes to small-scale subnetworks and genome-wide global networks. At each level, archaeal GRNs consist of a hybrid of bacterial, eukaryotic, and uniquely archaeal mechanisms. We discuss this theme from the perspective of the role of individual transcription factors in genome-wide regulation, how these proteins interact to compile GRN topological structures, and how these topologies lead to emergent, high-level GRN functions. We conclude by discussing how systems biology approaches are a fruitful avenue for addressing remaining challenges, such as discovering gene function and the evolution of GRNs.
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Affiliation(s)
| | - Peter D Tonner
- Department of Biology, Duke University, Durham, North Carolina 27708, USA.,Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA
| | - Cynthia L Darnell
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, North Carolina 27708, USA.,Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA;
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32
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Cerletti M, Giménez MI, Tröetschel C, D' Alessandro C, Poetsch A, De Castro RE, Paggi RA. Proteomic Study of the Exponential-Stationary Growth Phase Transition in the Haloarchaea Natrialba magadii and Haloferax volcanii. Proteomics 2018; 18:e1800116. [PMID: 29888524 DOI: 10.1002/pmic.201800116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/09/2018] [Indexed: 11/12/2022]
Abstract
The dynamic changes that take place along the phases of microbial growth (lag, exponential, stationary, and death) have been widely studied in bacteria at the molecular and cellular levels, but little is known for archaea. In this study, a high-throughput approach was used to analyze and compare the proteomes of two haloarchaea during exponential and stationary growth: the neutrophilic Haloferax volcanii and the alkaliphilic Natrialba magadii. Almost 2000 proteins were identified in each species (≈50% of the predicted proteome). Among them, 532 and 432 were found to be differential between growth phases in H. volcanii and N. magadii, respectively. Changes upon entrance into stationary phase included an overall increase in proteins involved in the transport of small molecules and ions, stress response, and fatty acid catabolism. Proteins related to genetic processes and cell division showed a notorious decrease in amount. The data reported in this study not only contributes to our understanding of the exponential-stationary growth phase transition in extremophilic archaea but also provides the first comprehensive analysis of the proteome composition of N. magadii. The MS proteomics data have been deposited in the ProteomeXchange Consortium with the dataset identifier JPST000395.
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Affiliation(s)
- Micaela Cerletti
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Mar del Plata, 7600, Argentina
| | - María Ines Giménez
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Mar del Plata, 7600, Argentina
| | | | - Celeste D' Alessandro
- Laboratório de Patologia e Controle Microbiano de Insetos, ESALQ-USP, Piracicaba-SP, 13418-900, Brazil
| | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum, Bochum, 44801, Germany.,School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth, PL4 8AA, United Kingdom
| | - Rosana Ester De Castro
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Mar del Plata, 7600, Argentina
| | - Roberto A Paggi
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Mar del Plata, 7600, Argentina
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An Archaeal Fluoride-Responsive Riboswitch Provides an Inducible Expression System for Hyperthermophiles. Appl Environ Microbiol 2018; 84:AEM.02306-17. [PMID: 29352088 DOI: 10.1128/aem.02306-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/07/2018] [Indexed: 12/12/2022] Open
Abstract
Robust genetic systems for the hyperthermophilic Thermococcales have facilitated the overexpression of native genes, enabled the addition of sequences encoding secretion signals, epitope, and affinity tags to coding regions, and aided the introduction of sequences encoding new proteins in these fast-growing fermentative heterotrophs. However, tightly controlled and easily manipulated systems facilitating regulated gene expression are limited for these hosts. Here, we describe an alternative method for regulatory control reliant on a cis-encoded functional riboswitch in the model archaeon Thermococcus kodakarensis Despite the hyperthermophilic growth temperatures, the proposed structure of the riboswitch conforms to a fluoride-responsive riboswitch encoded in many bacteria and similarly functions to regulate a component-conserved fluoride export pathway. Deleting components of the fluoride export pathway generates T. kodakarensis strains with increased fluoride sensitivity. The mechanism underlying regulated expression suggested that the riboswitch-encoding sequences could be utilized as a tunable expression cassette. When appended to a reporter gene, the riboswitch-mediated control system provides fluoride-dependent tunable regulatory potential, offering an alternative system for regulating gene expression. Riboswitch-regulated expression is thus ubiquitous in extant life and can be exploited to generate regulated expression systems for hyperthermophiles.IMPORTANCE Gene expression is controlled by a myriad of interconnected mechanisms that interpret metabolic states and environmental cues to balance cell physiology. Transcription regulation in Archaea is known to employ both typical repressors-operators and transcription activators to regulate transcription initiation in addition to the regulation afforded by chromatin structure. It was perhaps surprising that the presumed ancient mechanism of riboswitch-mediated regulation is found in Bacteria and Eukarya, but seemingly absent in Archaea We demonstrate here that a fluoride-responsive riboswitch functions to regulate a detoxification pathway in the hyperthermophilic archaeon Thermococcus kodakarensis The results obtained define a universal role for riboswitch-mediated regulation, adumbrate the presence of several riboswitch-regulated genes in Thermococcus kodakarensis, demonstrate the utility of RNA-based regulation at high temperatures, and provide a novel riboswitch-regulated expression system to employ in hyperthermophiles.
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Liu J, Li J, Dong H, Chen Y, Wang Y, Wu H, Li C, Weaver DT, Zhang L, Zhang B. Characterization of an Lrp/AsnC family regulator SCO3361, controlling actinorhodin production and morphological development in Streptomyces coelicolor. Appl Microbiol Biotechnol 2017; 101:5773-5783. [DOI: 10.1007/s00253-017-8339-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/06/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
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Le TN, Wagner A, Albers SV. A conserved hexanucleotide motif is important in UV-inducible promoters in Sulfolobus acidocaldarius. MICROBIOLOGY-SGM 2017; 163:778-788. [PMID: 28463103 PMCID: PMC5817253 DOI: 10.1099/mic.0.000455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Upon DNA damage, Sulfolobales exhibit a global gene regulatory response resulting in the expression of DNA transfer and repair proteins and the repression of the cell division machinery. Because the archaeal DNA damage response is still poorly understood, we investigated the promoters of the highly induced ups operon. Ups pili are involved in cellular aggregation and DNA exchange between cells. With LacS reporter gene assays we identified a conserved, non-palindromic hexanucleotide motif upstream of the ups core promoter elements to be essential for promoter activity. Substitution of this cis regulatory motif in the ups promoters resulted in abolishment of cellular aggregation and reduced DNA transfer. By screening the Sulfolobus acidocaldarius genome we identified a total of 214 genes harbouring the hexanucleotide motif in their respective promoter regions. Many of these genes were previously found to be regulated upon UV light treatment. Given the fact that the identified motif is conserved among S. acidocaldarius and Sulfolobus tokodaii promoters, we speculate that a common regulatory mechanism is present in these two species in response to DNA-damaging conditions.
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Affiliation(s)
- Thuong Ngoc Le
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Alexander Wagner
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
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Liu J, Chen Y, Wang W, Ren M, Wu P, Wang Y, Li C, Zhang L, Wu H, Weaver DT, Zhang B. Engineering of an Lrp family regulator SACE_Lrp improves erythromycin production in Saccharopolyspora erythraea. Metab Eng 2017; 39:29-37. [DOI: 10.1016/j.ymben.2016.10.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/05/2016] [Accepted: 10/25/2016] [Indexed: 01/09/2023]
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Transcription Factor-Mediated Gene Regulation in Archaea. RNA METABOLISM AND GENE EXPRESSION IN ARCHAEA 2017. [DOI: 10.1007/978-3-319-65795-0_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Novel stand-alone RAM domain protein-mediated catalytic control of anthranilate phosphoribosyltransferase in tryptophan biosynthesis in Thermus thermophilus. Extremophiles 2016; 21:73-83. [DOI: 10.1007/s00792-016-0884-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
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Global transcriptional regulator TrmB family members in prokaryotes. J Microbiol 2016; 54:639-45. [PMID: 27687225 DOI: 10.1007/s12275-016-6362-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/25/2016] [Accepted: 08/29/2016] [Indexed: 10/20/2022]
Abstract
Members of the TrmB family act as global transcriptional regulators for the activation or repression of sugar ABC transporters and central sugar metabolic pathways, including glycolytic, gluconeogenic, and other metabolic pathways, and also as chromosomal stabilizers in archaea. As a relatively newly classified transcriptional regulator family, there is limited experimental evidence for their role in Thermococcales, halophilic archaeon Halobacterium salinarum NRC1, and crenarchaea Sulfolobus strains, despite being one of the extending protein families in archaea. Recently, the protein structures of Pyrococcus furiosus TrmB and TrmBL2 were solved, and the transcriptomic data uncovered by microarray and ChIP-Seq were published. In the present review, recent evidence of the functional roles of TrmB family members in archaea is explained and extended to bacteria.
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Liu H, Wang K, Lindås AC, Peeters E. The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius. BMC Genomics 2016; 17:569. [PMID: 27502941 PMCID: PMC4977709 DOI: 10.1186/s12864-016-2890-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 07/06/2016] [Indexed: 01/09/2023] Open
Abstract
Background The Leucine-responsive Regulatory Protein (Lrp) family is a widespread family of regulatory transcription factors in prokaryotes. BarR is an Lrp-like transcription factor in the model archaeon Sulfolobus acidocaldarius that activates the expression of a β-alanine aminotransferase gene, which is involved in β-alanine degradation. In contrast to classical Lrp-like transcription factors, BarR is not responsive to any of the α-amino acids but interacts specifically with β-alanine. Besides the juxtaposed β-alanine aminotransferase gene, other regulatory targets of BarR have not yet been identified although β-alanine is the precursor of coenzyme A and thus an important central metabolite. The aim of this study is to extend the knowledge of the DNA-binding characteristics of BarR and of its corresponding regulon from a local to a genome-wide perspective. Results We characterized the genome-wide binding profile of BarR using chromatin immunoprecipation combined with high-throughput sequencing (ChIP-seq). This revealed 21 genomic binding loci. High-enrichment binding regions were validated to interact with purified BarR protein in vitro using electrophoretic mobility shift assays and almost all targets were also shown to harbour a conserved semi-palindromic binding motif. Only a small subset of enriched genomic sites are located in intergenic regions at a relative short distance to a promoter, and qRT-PCR analysis demonstrated that only one additional operon is under activation of BarR, namely the glutamine synthase operon. The latter is also a target of other Lrp-like transcription factors. Detailed inspection of the BarR ChIP-seq profile at the β-alanine aminotransferase promoter region in combination with binding motif predictions indicate that the operator structure is more complicated than previously anticipated, consisting of multiple (major and auxiliary) operators. Conclusions BarR has a limited regulon, and includes also glutamine synthase genes besides the previously characterized β-alanine aminotransferase. Regulation of glutamine synthase is suggestive of a link between β-alanine and α-amino acid metabolism in S. acidocaldarius. Furthermore, this work reveals that the BarR regulon overlaps with that of other Lrp-like regulators. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2890-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Han Liu
- Department of Bio-Engineering Sciences, Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Kun Wang
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius v. 20C, SE-10691, Stockholm, Sweden
| | - Ann-Christin Lindås
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius v. 20C, SE-10691, Stockholm, Sweden
| | - Eveline Peeters
- Department of Bio-Engineering Sciences, Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.
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Raut MP, Couto N, Pham TK, Evans C, Noirel J, Wright PC. Quantitative proteomic analysis of the influence of lignin on biofuel production by Clostridium acetobutylicum ATCC 824. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:113. [PMID: 27247624 PMCID: PMC4886415 DOI: 10.1186/s13068-016-0523-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 05/09/2016] [Indexed: 05/30/2023]
Abstract
BACKGROUND Clostridium acetobutylicum has been a focus of research because of its ability to produce high-value compounds that can be used as biofuels. Lignocellulose is a promising feedstock, but the lignin-cellulose-hemicellulose biomass complex requires chemical pre-treatment to yield fermentable saccharides, including cellulose-derived cellobiose, prior to bioproduction of acetone-butanol-ethanol (ABE) and hydrogen. Fermentation capability is limited by lignin and thus process optimization requires knowledge of lignin inhibition. The effects of lignin on cellular metabolism were evaluated for C. acetobutylicum grown on medium containing either cellobiose only or cellobiose plus lignin. Microscopy, gas chromatography and 8-plex iTRAQ-based quantitative proteomic technologies were applied to interrogate the effect of lignin on cellular morphology, fermentation and the proteome. RESULTS Our results demonstrate that C. acetobutylicum has reduced performance for solvent production when lignin is present in the medium. Medium supplemented with 1 g L(-1) of lignin led to delay and decreased solvents production (ethanol; 0.47 g L(-1) for cellobiose and 0.27 g L(-1) for cellobiose plus lignin and butanol; 0.13 g L(-1) for cellobiose and 0.04 g L(-1) for cellobiose plus lignin) at 20 and 48 h, respectively, resulting in the accumulation of acetic acid and butyric acid. Of 583 identified proteins (FDR < 1 %), 328 proteins were quantified with at least two unique peptides. Up- or down-regulation of protein expression was determined by comparison of exponential and stationary phases of cellobiose in the presence and absence of lignin. Of relevance, glycolysis and fermentative pathways were mostly down-regulated, during exponential and stationary growth phases in presence of lignin. Moreover, proteins involved in DNA repair, transcription/translation and GTP/ATP-dependent activities were also significantly affected and these changes were associated with altered cell morphology. CONCLUSIONS This is the first comprehensive analysis of the cellular responses of C. acetobutylicum to lignin at metabolic and physiological levels. These data will enable targeted metabolic engineering strategies to optimize biofuel production from biomass by overcoming limitations imposed by the presence of lignin.
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Affiliation(s)
- Mahendra P. Raut
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Narciso Couto
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Trong K. Pham
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Caroline Evans
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Josselin Noirel
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
- />Chaire de Bioinformatique, LGBA, Conservatoire National Des Arts Et Métiers, 75003 Paris, France
| | - Phillip C. Wright
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
- />School of Chemical Engineering and Advanced Materials, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
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Wang X, An C, Yang M, Li X, Ke Y, Lei S, Xu X, Yu J, Ren H, Du X, Wang Z, Qiu Y, Liu B, Chen Z. Immunization with individual proteins of the Lrp/AsnC family induces protection against Brucella melitensis 16M challenges in mice. Front Microbiol 2015; 6:1193. [PMID: 26579099 PMCID: PMC4625564 DOI: 10.3389/fmicb.2015.01193] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/13/2015] [Indexed: 11/13/2022] Open
Abstract
Brucellosis is one of the most common zoonoses worldwide. Subunit vaccines are promising for the prevention of human brucellosis. In our previous protective antigen screening studies, we identified a new protective antigen, BMEI0357, which belongs to the Lrp/asnC protein family, a conserved transcriptional regulator in bacteria that is absent in eukaryotes. In the present study, the Brucella genome annotation was screened and a total of six proteins were identified as members of the Lrp/AsnC family. Lrp/AsnC proteins have two domains that are conserved among the family members. However, sequence similarities between these proteins ranged from 9 to 50%, indicating high sequence heterogeneity. To test whether proteins of this family have similar characteristics, all six proteins were cloned and expressed in Escherichia coli. The recombinant proteins were purified and their protective efficacy was evaluated in BALB/c mice challenged with Brucella melitensis 16M. The results show that all six Lrp/AsnC proteins could induce a protective immune response against Brucella melitensis 16M. Antibodies against the Lrp/AsnC proteins were detected in the immunized mice. However, levels of antibodies against these proteins were relatively variable in human brucellosis sera. Taken together, our results show that these six proteins of the Lrp/AsnC family in Brucella could induce protective immune responses in mice.
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Affiliation(s)
- Xinhui Wang
- Key Laboratory of Zoonosis, Institute of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University Changchun, China ; Experimental Animal Center, Academy of Military Medical Sciences Beijing, China ; Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Chang An
- Key Laboratory of Zoonosis, Institute of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University Changchun, China ; Experimental Animal Center, Academy of Military Medical Sciences Beijing, China
| | - Mingjuan Yang
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xinran Li
- Key Laboratory of Zoonosis, Institute of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University Changchun, China ; Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Yuehua Ke
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Shuangshuang Lei
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xiaoyang Xu
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Jiuxuan Yu
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Hang Ren
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xinying Du
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Zhoujia Wang
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Yefeng Qiu
- Experimental Animal Center, Academy of Military Medical Sciences Beijing, China
| | - Bo Liu
- Key Laboratory of Zoonosis, Institute of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University Changchun, China
| | - Zeliang Chen
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
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Romero-Rodríguez A, Robledo-Casados I, Sánchez S. An overview on transcriptional regulators in Streptomyces. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1017-39. [PMID: 26093238 DOI: 10.1016/j.bbagrm.2015.06.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 12/19/2022]
Abstract
Streptomyces are Gram-positive microorganisms able to adapt and respond to different environmental conditions. It is the largest genus of Actinobacteria comprising over 900 species. During their lifetime, these microorganisms are able to differentiate, produce aerial mycelia and secondary metabolites. All of these processes are controlled by subtle and precise regulatory systems. Regulation at the transcriptional initiation level is probably the most common for metabolic adaptation in bacteria. In this mechanism, the major players are proteins named transcription factors (TFs), capable of binding DNA in order to repress or activate the transcription of specific genes. Some of the TFs exert their action just like activators or repressors, whereas others can function in both manners, depending on the target promoter. Generally, TFs achieve their effects by using one- or two-component systems, linking a specific type of environmental stimulus to a transcriptional response. After DNA sequencing, many streptomycetes have been found to have chromosomes ranging between 6 and 12Mb in size, with high GC content (around 70%). They encode for approximately 7000 to 10,000 genes, 50 to 100 pseudogenes and a large set (around 12% of the total chromosome) of regulatory genes, organized in networks, controlling gene expression in these bacteria. Among the sequenced streptomycetes reported up to now, the number of transcription factors ranges from 471 to 1101. Among these, 315 to 691 correspond to transcriptional regulators and 31 to 76 are sigma factors. The aim of this work is to give a state of the art overview on transcription factors in the genus Streptomyces.
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Affiliation(s)
- Alba Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Ivonne Robledo-Casados
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico.
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Peeters E, Driessen RPC, Werner F, Dame RT. The interplay between nucleoid organization and transcription in archaeal genomes. Nat Rev Microbiol 2015; 13:333-41. [PMID: 25944489 DOI: 10.1038/nrmicro3467] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The archaeal genome is organized by either eukaryotic-like histone proteins or bacterial-like nucleoid-associated proteins. Recent studies have revealed novel insights into chromatin dynamics and their effect on gene expression in archaeal model organisms. In this Progress article, we discuss the interplay between chromatin proteins, such as histones and Alba, and components of the basal transcription machinery, as well as between chromatin structure and gene-specific transcription factors in archaea. Such an interplay suggests that chromatin might have a role in regulating gene expression on both a global and a gene-specific level. Moreover, several archaeal transcription factors combine a global gene regulatory role with an architectural role, thus contributing to chromatin organization and compaction, as well as gene expression. We describe the emerging principles underlying how these factors cooperate in nucleoid structuring and gene regulation.
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Affiliation(s)
- Eveline Peeters
- 1] Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium. [2]
| | - Rosalie P C Driessen
- 1] Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands. [2]
| | - Finn Werner
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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Cerletti M, Paggi RA, Guevara CR, Poetsch A, De Castro RE. Global role of the membrane protease LonB in Archaea: Potential protease targets revealed by quantitative proteome analysis of a lonB mutant in Haloferax volcanii. J Proteomics 2015; 121:1-14. [PMID: 25829260 DOI: 10.1016/j.jprot.2015.03.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/04/2015] [Accepted: 03/12/2015] [Indexed: 02/07/2023]
Abstract
UNLABELLED The membrane-associated LonB protease is essential for viability in Haloferax volcanii, however, the cellular processes affected by this protease in archaea are unknown. In this study, the impact of a lon conditional mutation (down-regulation) on H. volcanii physiology was examined by comparing proteomes of parental and mutant cells using shotgun proteomics. A total of 1778 proteins were identified (44% of H. volcanii predicted proteome) and 142 changed significantly in amount (≥2 fold). Of these, 66 were augmented in response to Lon deficiency suggesting they could be Lon substrates. The "Lon subproteome" included soluble and predicted membrane proteins expected to participate in diverse cellular processes. The dramatic stabilization of phytoene synthase (57 fold) in concert with overpigmentation of lon mutant cells suggests that Lon controls carotenogenesis in H. volcanii. Several hypothetical proteins, which may reveal novel functions and/or be involved in adaptation to extreme environments, were notably increased (300 fold). This study, which represents the first proteome examination of a Lon deficient archaeal cell, shows that Lon has a strong impact on H. volcanii physiology evidencing the cellular processes controlled by this protease in Archaea. Additionally, this work provides a platform for the discovery of novel targets of Lon proteases. BIOLOGICAL SIGNIFICANCE The proteome of a Lon-deficient archaeal cell was examined for the first time showing that Lon has a strong impact on H. volcanii physiology and evidencing the proteins and cellular processes controlled by this protease in Archaea. This work will facilitate future investigations aiming to address Lon function in archaea and provides a platform for the discovery of endogenous targets of the archaeal-type Lon as well as novel targets/processes regulated by Lon proteases. This knowledge will advance the understanding on archaeal physiology and the biological function of membrane proteases in microorganisms.
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Affiliation(s)
- Micaela Cerletti
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3250 4to nivel, Mar del Plata (7600), Argentina
| | - Roberto A Paggi
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3250 4to nivel, Mar del Plata (7600), Argentina
| | | | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Rosana E De Castro
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3250 4to nivel, Mar del Plata (7600), Argentina.
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Plaisier CL, Lo FY, Ashworth J, Brooks AN, Beer KD, Kaur A, Pan M, Reiss DJ, Facciotti MT, Baliga NS. Evolution of context dependent regulation by expansion of feast/famine regulatory proteins. BMC SYSTEMS BIOLOGY 2014; 8:122. [PMID: 25394904 PMCID: PMC4236453 DOI: 10.1186/s12918-014-0122-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/16/2014] [Indexed: 11/25/2022]
Abstract
Background Expansion of transcription factors is believed to have played a crucial role in evolution of all organisms by enabling them to deal with dynamic environments and colonize new environments. We investigated how the expansion of the Feast/Famine Regulatory Protein (FFRP) or Lrp-like proteins into an eight-member family in Halobacterium salinarum NRC-1 has aided in niche-adaptation of this archaeon to a complex and dynamically changing hypersaline environment. Results We mapped genome-wide binding locations for all eight FFRPs, investigated their preference for binding different effector molecules, and identified the contexts in which they act by analyzing transcriptional responses across 35 growth conditions that mimic different environmental and nutritional conditions this organism is likely to encounter in the wild. Integrative analysis of these data constructed an FFRP regulatory network with conditionally active states that reveal how interrelated variations in DNA-binding domains, effector-molecule preferences, and binding sites in target gene promoters have tuned the functions of each FFRP to the environments in which they act. We demonstrate how conditional regulation of similar genes by two FFRPs, AsnC (an activator) and VNG1237C (a repressor), have striking environment-specific fitness consequences for oxidative stress management and growth, respectively. Conclusions This study provides a systems perspective into the evolutionary process by which gene duplication within a transcription factor family contributes to environment-specific adaptation of an organism. Electronic supplementary material The online version of this article (doi:10.1186/s12918-014-0122-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Fang-Yin Lo
- Institute for Systems Biology, Seattle, WA, USA. .,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
| | | | - Aaron N Brooks
- Institute for Systems Biology, Seattle, WA, USA. .,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
| | - Karlyn D Beer
- Institute for Systems Biology, Seattle, WA, USA. .,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
| | | | - Min Pan
- Institute for Systems Biology, Seattle, WA, USA.
| | | | - Marc T Facciotti
- Department of Biomedical Engineering, University of California, Davis, CA, USA. .,Genome Center, University of California, Davis, CA, USA.
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, USA. .,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA. .,Department of Microbiology, University of Washington, Seattle, WA, USA. .,Department of Biology, University of Washington, Seattle, WA, USA.
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Ashworth J, Plaisier CL, Lo FY, Reiss DJ, Baliga NS. Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction. PLoS One 2014; 9:e107863. [PMID: 25255272 PMCID: PMC4177876 DOI: 10.1371/journal.pone.0107863] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 08/16/2014] [Indexed: 11/18/2022] Open
Abstract
Widespread microbial genome sequencing presents an opportunity to understand the gene regulatory networks of non-model organisms. This requires knowledge of the binding sites for transcription factors whose DNA-binding properties are unknown or difficult to infer. We adapted a protein structure-based method to predict the specificities and putative regulons of homologous transcription factors across diverse species. As a proof-of-concept we predicted the specificities and transcriptional target genes of divergent archaeal feast/famine regulatory proteins, several of which are encoded in the genome of Halobacterium salinarum. This was validated by comparison to experimentally determined specificities for transcription factors in distantly related extremophiles, chromatin immunoprecipitation experiments, and cis-regulatory sequence conservation across eighteen related species of halobacteria. Through this analysis we were able to infer that Halobacterium salinarum employs a divergent local trans-regulatory strategy to regulate genes (carA and carB) involved in arginine and pyrimidine metabolism, whereas Escherichia coli employs an operon. The prediction of gene regulatory binding sites using structure-based methods is useful for the inference of gene regulatory relationships in new species that are otherwise difficult to infer.
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Affiliation(s)
- Justin Ashworth
- Institute for Systems Biology, Seattle, Washington, United States of America
- * E-mail: (JA); (NB)
| | | | - Fang Yin Lo
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - David J. Reiss
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (JA); (NB)
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48
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Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol Mol Biol Rev 2014; 78:89-175. [PMID: 24600042 DOI: 10.1128/mmbr.00041-13] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The metabolism of Archaea, the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya. However, this metabolic complexity in Archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of "new," unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea. In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya. Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.
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Liu H, Orell A, Maes D, van Wolferen M, Lindås AC, Bernander R, Albers SV, Charlier D, Peeters E. BarR, an Lrp-type transcription factor in Sulfolobus acidocaldarius, regulates an aminotransferase gene in a β-alanine responsive manner. Mol Microbiol 2014; 92:625-39. [PMID: 24646198 DOI: 10.1111/mmi.12583] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2014] [Indexed: 12/29/2022]
Abstract
In archaea, nothing is known about the β-alanine degradation pathway or its regulation. In this work, we identify and characterize BarR, a novel Lrp-like transcription factor and the first one that has a non-proteinogenic amino acid ligand. BarR is conserved in Sulfolobus acidocaldarius and Sulfolobus tokodaii and is located in a divergent operon with a gene predicted to encode β-alanine aminotransferase. Deletion of barR resulted in a reduced exponential growth rate in the presence of β-alanine. Furthermore, qRT-PCR and promoter activity assays demonstrated that BarR activates the expression of the adjacent aminotransferase gene, but only upon β-alanine supplementation. In contrast, auto-activation proved to be β-alanine independent. Heterologously produced BarR is an octamer in solution and forms a single complex by interacting with multiple sites in the 170 bp long intergenic region separating the divergently transcribed genes. In vitro, DNA binding is specifically responsive to β-alanine and site-mutant analyses indicated that β-alanine directly interacts with the ligand-binding pocket. Altogether, this work contributes to the growing body of evidence that in archaea, Lrp-like transcription factors have physiological roles that go beyond the regulation of α-amino acid metabolism.
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Affiliation(s)
- Han Liu
- Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
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50
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Abstract
The ability of organisms to sense and respond to their environment is essential to their survival. This is no different for members of the third domain of life, the Archaea. Archaea are found in diverse and often extreme habitats. However, their ability to sense and respond to their environment at the level of gene expression has been understudied when compared to bacteria and eukaryotes. Over the last decade, the field has expanded, and a variety of unique and interesting regulatory schemes have been unraveled. In this review, the current state of knowledge of archaeal transcription regulation is explored.
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