1
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Liu LM, Sun CY, Xi YC, Lu XH, Yong CW, Li SQ, Sun QW, Wang XW, Mao YZ, Chen W, Jiang HB. A global transcriptional activator involved in the iron homeostasis in cyanobacteria. SCIENCE ADVANCES 2024; 10:eadl6428. [PMID: 38959319 PMCID: PMC11221513 DOI: 10.1126/sciadv.adl6428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
Cyanobacteria use a series of adaptation strategies and a complicated regulatory network to maintain intracellular iron (Fe) homeostasis. Here, a global activator named IutR has been identified through three-dimensional chromosome organization and transcriptome analysis in a model cyanobacterium Synechocystis sp. PCC 6803. Inactivation of all three homologous IutR-encoding genes resulted in an impaired tolerance of Synechocystis to Fe deficiency and loss of the responses of Fe uptake-related genes to Fe-deplete conditions. Protein-promoter interaction assays confirmed the direct binding of IutR with the promoters of genes related to Fe uptake, and chromatin immunoprecipitation sequencing analysis further revealed that in addition to Fe uptake, IutR could regulate many other physiological processes involved in intracellular Fe homeostasis. These results proved that IutR is an important transcriptional activator, which is essential for cyanobacteria to induce Fe-deficiency response genes. This study provides in-depth insights into the complicated Fe-deficient signaling network and the molecular mechanism of cyanobacteria adaptation to Fe-deficient environments.
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Affiliation(s)
- Ling-Mei Liu
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Chuan-Yu Sun
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Yi-Cao Xi
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Xiao-Hui Lu
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Cheng-Wen Yong
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Shuang-Qing Li
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Qiao-Wei Sun
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Xin-Wei Wang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - You-Zhi Mao
- Wuhan Frasergen Bioinformatics Co. Ltd., Wuhan, Hubei, China
| | - Weizhong Chen
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Hai-Bo Jiang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
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2
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Sarasa-Buisan C, Guío J, Peleato ML, Fillat MF, Sevilla E. Expanding the FurC (PerR) regulon in Anabaena (Nostoc) sp. PCC 7120: Genome-wide identification of novel direct targets uncovers FurC participation in central carbon metabolism regulation. PLoS One 2023; 18:e0289761. [PMID: 37549165 PMCID: PMC10406281 DOI: 10.1371/journal.pone.0289761] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
FurC (PerR, Peroxide Response Regulator) from Anabaena sp. PCC 7120 (also known as Nostoc sp. PCC 7120) is a master regulator engaged in the modulation of relevant processes including the response to oxidative stress, photosynthesis and nitrogen fixation. Previous differential gene expression analysis of a furC-overexpressing strain (EB2770FurC) allowed the inference of a putative FurC DNA-binding consensus sequence. In the present work, more data concerning the regulon of the FurC protein were obtained through the searching of the putative FurC-box in the whole Anabaena sp. PCC 7120 genome. The total amount of novel FurC-DNA binding sites found in the promoter regions of genes with known function was validated by electrophoretic mobility shift assays (EMSA) identifying 22 new FurC targets. Some of these identified targets display relevant roles in nitrogen fixation (hetR and hgdC) and carbon assimilation processes (cmpR, glgP1 and opcA), suggesting that FurC could be an additional player for the harmonization of carbon and nitrogen metabolisms. Moreover, differential gene expression of a selection of newly identified FurC targets was measured by Real Time RT-PCR in the furC-overexpressing strain (EB2770FurC) comparing to Anabaena sp. PCC 7120 revealing that in most of these cases FurC could act as a transcriptional activator.
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Affiliation(s)
- Cristina Sarasa-Buisan
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - Jorge Guío
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - M. Luisa Peleato
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - María F. Fillat
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - Emma Sevilla
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
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3
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Enzingmüller-Bleyl TC, Boden JS, Herrmann AJ, Ebel KW, Sánchez-Baracaldo P, Frankenberg-Dinkel N, Gehringer MM. On the trail of iron uptake in ancestral Cyanobacteria on early Earth. GEOBIOLOGY 2022; 20:776-789. [PMID: 35906866 DOI: 10.1111/gbi.12515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacteria oxygenated Earth's atmosphere ~2.4 billion years ago, during the Great Oxygenation Event (GOE), through oxygenic photosynthesis. Their high iron requirement was presumably met by high levels of Fe(II) in the anoxic Archean environment. We found that many deeply branching Cyanobacteria, including two Gloeobacter and four Pseudanabaena spp., cannot synthesize the Fe(II) specific transporter, FeoB. Phylogenetic and relaxed molecular clock analyses find evidence that FeoB and the Fe(III) transporters, cFTR1 and FutB, were present in Proterozoic, but not earlier Archaean lineages of Cyanobacteria. Furthermore Pseudanabaena sp. PCC7367, an early diverging marine, benthic strain grown under simulated Archean conditions, constitutively expressed cftr1, even after the addition of Fe(II). Our genetic profiling suggests that, prior to the GOE, ancestral Cyanobacteria may have utilized alternative metal iron transporters such as ZIP, NRAMP, or FicI, and possibly also scavenged exogenous siderophore bound Fe(III), as they only acquired the necessary Fe(II) and Fe(III) transporters during the Proterozoic. Given that Cyanobacteria arose 3.3-3.6 billion years ago, it is possible that limitations in iron uptake may have contributed to the delay in their expansion during the Archean, and hence the oxygenation of the early Earth.
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Affiliation(s)
| | - Joanne S Boden
- School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, UK
- School of Earth and Environmental Sciences, University of St. Andrews, St. Andrews, UK
| | - Achim J Herrmann
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Katharina W Ebel
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | | | - Michelle M Gehringer
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
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4
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Selão TT. Exploring cyanobacterial diversity for sustainable biotechnology. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3057-3071. [PMID: 35467729 DOI: 10.1093/jxb/erac053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Cyanobacteria are an evolutionarily ancient and diverse group of microorganisms. Their genetic diversity has
allowed them to occupy and play vital roles in a wide range of ecological niches, from desert soil crusts to tropical oceans. Owing to bioprospecting efforts and the development of new platform technologies enabling their study and manipulation, our knowledge of cyanobacterial metabolism is rapidly expanding. This review explores our current understanding of the genetic and metabolic features of cyanobacteria, from the more established cyanobacterial model strains to the newly isolated/described species, particularly the fast-growing, highly productive, and genetically amenable strains, as promising chassis for renewable biotechnology. It also discusses emerging technologies for their study and manipulation, enabling researchers to harness the astounding diversity of the cyanobacterial genomic and metabolic treasure trove towards the establishment of a sustainable bioeconomy.
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Affiliation(s)
- Tiago Toscano Selão
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
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5
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Sarasa-Buisan C, Guio J, Broset E, Peleato ML, Fillat MF, Sevilla E. FurC (PerR) from Anabaena sp. PCC7120: a versatile transcriptional regulator engaged in the regulatory network of heterocyst development and nitrogen fixation. Environ Microbiol 2021; 24:566-582. [PMID: 33938105 DOI: 10.1111/1462-2920.15552] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/19/2021] [Accepted: 04/30/2021] [Indexed: 11/29/2022]
Abstract
FurC (PerR) from Anabaena sp. PCC7120 was previously described as a key transcriptional regulator involved in setting off the oxidative stress response. In the last years, the cross-talk between oxidative stress, iron homeostasis and nitrogen metabolism is becoming more and more evident. In this work, the transcriptome of a furC-overexpressing strain was compared with that of a wild-type strain under both standard and nitrogen-deficiency conditions. The results showed that the overexpression of furC deregulates genes involved in several categories standing out photosynthesis, iron transport and nitrogen metabolism. The novel FurC-direct targets included some regulatory elements that control heterocyst development (hetZ and asr1734), genes directly involved in the heterocyst envelope formation (devBCA and hepC) and genes which participate in the nitrogen fixation process (nifHDK and nifH2, rbrA rubrerythrin and xisHI excisionase). Likewise, furC overexpression notably impacts the mRNA levels of patA encoding a key protein in the heterocyst pattern formation. The relevance of FurC in these processes is bringing out by the fact that the overexpression of furC impairs heterocyst development and cell growth under nitrogen step-down conditions. In summary, this work reveals a new player in the complex regulatory network of heterocyst formation and nitrogen fixation.
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Affiliation(s)
- Cristina Sarasa-Buisan
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Pedro Cerbuna 12, Zaragoza, 50009, Spain
| | - Jorge Guio
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Pedro Cerbuna 12, Zaragoza, 50009, Spain
| | - Esther Broset
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Pedro Cerbuna 12, Zaragoza, 50009, Spain
| | - M Luisa Peleato
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Pedro Cerbuna 12, Zaragoza, 50009, Spain
| | - María F Fillat
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Pedro Cerbuna 12, Zaragoza, 50009, Spain
| | - Emma Sevilla
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Pedro Cerbuna 12, Zaragoza, 50009, Spain
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6
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Guío J, Sarasa-Buisan C, Velázquez-Campoy A, Bes MT, Fillat MF, Peleato ML, Sevilla E. 2-oxoglutarate modulates the affinity of FurA for the ntcA promoter in Anabaena sp. PCC 7120. FEBS Lett 2019; 594:278-289. [PMID: 31538336 DOI: 10.1002/1873-3468.13610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/13/2019] [Accepted: 09/14/2019] [Indexed: 11/11/2022]
Abstract
2-oxoglutarate (2-OG) is a central metabolite that acts as a signaling molecule informing about the status of the carbon/nitrogen balance of the cell. In recent years, some transcriptional regulators and even two-component systems have been described as 2-OG sensors. In the nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120, two master regulators, NtcA and FurA, are deeply involved in the regulation of nitrogen metabolism. Both of them show a complex intertwined regulatory circuit to achieve a suitable regulation of nitrogen fixation. In this work, 2-OG is found to bind FurA, modulating the specific binding of FurA to the ntcA promoter. This study provides evidence of a new additional control point in the complex network controlled by the NtcA and FurA proteins.
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Affiliation(s)
- Jorge Guío
- Departamento de Bioquímica y Biología Molecular y Celular, Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Spain
| | - Cristina Sarasa-Buisan
- Departamento de Bioquímica y Biología Molecular y Celular, Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain.,Fundacion ARAID, Government of Aragon, Zaragoza, Spain
| | - María Teresa Bes
- Departamento de Bioquímica y Biología Molecular y Celular, Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Spain
| | - María F Fillat
- Departamento de Bioquímica y Biología Molecular y Celular, Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Spain
| | - María Luisa Peleato
- Departamento de Bioquímica y Biología Molecular y Celular, Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Spain
| | - Emma Sevilla
- Departamento de Bioquímica y Biología Molecular y Celular, Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Spain
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7
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Kaushik MS, Mishra AK. Iron deficiency influences NtcA-dependent regulation of fatty acid desaturation and heterocyte envelop formation in Anabaena sp. PCC 7120. PHYSIOLOGIA PLANTARUM 2019; 166:570-584. [PMID: 30035317 DOI: 10.1111/ppl.12806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 07/09/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
In Anabaena sp. PCC 7120, iron is an essential trace element and its availability determines proper functioning of several kinds of metabolisms. Iron deficiency leads to several unavoidable consequences including membrane damage. In the present study, we dealt with the impact of iron deficiency on NtcA (global nitrogen regulator)-dependent regulation of two important processes, i.e. fatty acid desaturation and heterocyte envelop formation in cyanobacterium Anabaena sp. PCC 7120. In Anabaena sp. PCC 7120, NtcA regulates fatty acid desaturation by regulating enzyme fatty acid desaturases. The NtcA-based regulation of fatty acid desaturation may be direct or indirect. Furthermore, the expression of genes involved in the heterocyte envelope polysaccharide (HEP) layer formation (hepABCK) and heterocyte-specific glycolipids (HGLs) synthesis (devH, hglEA , prpJ and devB) were also under the control of NtcA and reduced under iron deficiency background. The enhanced expression of furA and early downregulation of ntcA under iron deficiency is responsible for reduction in fatty acid desaturation as well as decrease in the expression of genes involved in HEP layer formation and HGL synthesis. Overall results confirmed that iron deficiency influences the NtcA-based regulation of fatty acid desaturation and heterocyte envelop formation in Anabaena sp. PCC 7120.
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Affiliation(s)
- Manish S Kaushik
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Arun K Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
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8
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Sevilla E, Bes MT, González A, Peleato ML, Fillat MF. Redox-Based Transcriptional Regulation in Prokaryotes: Revisiting Model Mechanisms. Antioxid Redox Signal 2019; 30:1651-1696. [PMID: 30073850 DOI: 10.1089/ars.2017.7442] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
SIGNIFICANCE The successful adaptation of microorganisms to ever-changing environments depends, to a great extent, on their ability to maintain redox homeostasis. To effectively maintain the redox balance, cells have developed a variety of strategies mainly coordinated by a battery of transcriptional regulators through diverse mechanisms. Recent Advances: This comprehensive review focuses on the main mechanisms used by major redox-responsive regulators in prokaryotes and their relationship with the different redox signals received by the cell. An overview of the corresponding regulons is also provided. CRITICAL ISSUES Some regulators are difficult to classify since they may contain several sensing domains and respond to more than one signal. We propose a classification of redox-sensing regulators into three major groups. The first group contains one-component or direct regulators, whose sensing and regulatory domains are in the same protein. The second group comprises the classical two-component systems involving a sensor kinase that transduces the redox signal to its DNA-binding partner. The third group encompasses a heterogeneous group of flavin-based photosensors whose mechanisms are not always fully understood and are often involved in more complex regulatory networks. FUTURE DIRECTIONS Redox-responsive transcriptional regulation is an intricate process as identical signals may be sensed and transduced by different transcription factors, which often interplay with other DNA-binding proteins with or without regulatory activity. Although there is much information about some key regulators, many others remain to be fully characterized due to the instability of their clusters under oxygen. Understanding the mechanisms and the regulatory networks operated by these regulators is essential for the development of future applications in biotechnology and medicine.
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Affiliation(s)
- Emma Sevilla
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María Teresa Bes
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Andrés González
- 2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain.,4 Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - María Luisa Peleato
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María F Fillat
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
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9
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Formation and maintenance of nitrogen-fixing cell patterns in filamentous cyanobacteria. Proc Natl Acad Sci U S A 2016; 113:6218-23. [PMID: 27162328 DOI: 10.1073/pnas.1524383113] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cyanobacteria forming one-dimensional filaments are paradigmatic model organisms of the transition between unicellular and multicellular living forms. Under nitrogen-limiting conditions, in filaments of the genus Anabaena, some cells differentiate into heterocysts, which lose the possibility to divide but are able to fix environmental nitrogen for the colony. These heterocysts form a quasiregular pattern in the filament, representing a prototype of patterning and morphogenesis in prokaryotes. Recent years have seen advances in the identification of the molecular mechanism regulating this pattern. We use these data to build a theory on heterocyst pattern formation, for which both genetic regulation and the effects of cell division and filament growth are key components. The theory is based on the interplay of three generic mechanisms: local autoactivation, early long-range inhibition, and late long-range inhibition. These mechanisms can be identified with the dynamics of hetR, patS, and hetN expression. Our theory reproduces quantitatively the experimental dynamics of pattern formation and maintenance for wild type and mutants. We find that hetN alone is not enough to play the role as the late inhibitory mechanism: a second mechanism, hypothetically the products of nitrogen fixation supplied by heterocysts, must also play a role in late long-range inhibition. The preponderance of even intervals between heterocysts arises naturally as a result of the interplay between the timescales of genetic regulation and cell division. We also find that a purely stochastic initiation of the pattern, without a two-stage process, is enough to reproduce experimental observations.
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10
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González A, Sevilla E, Bes MT, Peleato ML, Fillat MF. Pivotal Role of Iron in the Regulation of Cyanobacterial Electron Transport. Adv Microb Physiol 2016; 68:169-217. [PMID: 27134024 DOI: 10.1016/bs.ampbs.2016.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron-containing metalloproteins are the main cornerstones for efficient electron transport in biological systems. The abundance and diversity of iron-dependent proteins in cyanobacteria makes those organisms highly dependent of this micronutrient. To cope with iron imbalance, cyanobacteria have developed a survey of adaptation strategies that are strongly related to the regulation of photosynthesis, nitrogen metabolism and other central electron transfer pathways. Furthermore, either in its ferrous form or as a component of the haem group, iron plays a crucial role as regulatory signalling molecule that directly or indirectly modulates the composition and efficiency of cyanobacterial redox reactions. We present here the major mechanism used by cyanobacteria to couple iron homeostasis to the regulation of electron transport, making special emphasis in processes specific in those organisms.
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Affiliation(s)
| | - E Sevilla
- University of Zaragoza, Zaragoza, Spain
| | - M T Bes
- University of Zaragoza, Zaragoza, Spain
| | | | - M F Fillat
- University of Zaragoza, Zaragoza, Spain.
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11
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Expanding the Role of FurA as Essential Global Regulator in Cyanobacteria. PLoS One 2016; 11:e0151384. [PMID: 26967347 PMCID: PMC4788461 DOI: 10.1371/journal.pone.0151384] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/26/2016] [Indexed: 01/03/2023] Open
Abstract
In the nitrogen-fixing heterocyst-forming cyanobacterium Anabaena sp. PCC 7120, the ferric uptake regulator FurA plays a global regulatory role. Failures to eliminate wild-type copies of furA gene from the polyploid genome suggest essential functions. In the present study, we developed a selectively regulated furA expression system by the replacement of furA promoter in the Anabaena sp. chromosomes with the Co2+/Zn2+ inducible coaT promoter from Synechocystis sp. PCC 6803. By removing Co2+ and Zn2+ from the medium and shutting off furA expression, we showed that FurA was absolutely required for cyanobacterial growth. RNA-seq based comparative transcriptome analyses of the furA-turning off strain and its parental wild-type in conjunction with subsequent electrophoretic mobility shift assays and semi-quantitative RT-PCR were carried out in order to identify direct transcriptional targets and unravel new biological roles of FurA. The results of such approaches led us to identify 15 novel direct iron-dependent transcriptional targets belonging to different functional categories including detoxification and defences against oxidative stress, phycobilisome degradation, chlorophyll catabolism and programmed cell death, light sensing and response, heterocyst differentiation, exopolysaccharide biosynthesis, among others. Our analyses evidence novel interactions in the complex regulatory network orchestrated by FurA in cyanobacteria.
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12
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Song L, Li T, Fan L, Shen XY, Hou CL. Identification and Evaluation of Reliable Reference Genes in the Medicinal Fungus Shiraia bambusicola. Curr Microbiol 2015; 72:444-9. [PMID: 26721832 DOI: 10.1007/s00284-015-0972-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 11/11/2015] [Indexed: 01/12/2023]
Abstract
The stability of reference genes plays a vital role in real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis, which is generally regarded as a convenient and sensitive tool for the analysis of gene expression. A well-known medicinal fungus, Shiraia bambusicola, has great potential in the pharmaceutical, agricultural and food industries, but its suitable reference genes have not yet been determined. In the present study, 11 candidate reference genes in S. bambusicola were first evaluated and validated comprehensively. To identify the suitable reference genes for qRT-PCR analysis, three software-based algorithms, geNorm, NormFinder and Best Keeper, were applied to rank the tested genes. RNA samples were collected from seven fermentation stages using different media (potato dextrose or Czapek medium) and under different light conditions (12-h light/12-h dark and all-dark). The three most appropriate reference genes, ubi, tfc and ags, were able to normalize the qRT-PCR results under the culturing conditions of 12-h light/12-h dark, whereas the other three genes, vac, gke and acyl, performed better in the culturing conditions of all-dark growth. Therefore, under different light conditions, at least two reference genes (ubi and vac) could be employed to assure the reliability of qRT-PCR results. For both the natural culture medium (the most appropriate genes of this group: ubi, tfc and ags) and the chemically defined synthetic medium (the most stable genes of this group: tfc, vac and ef), the tfc gene remained the best gene used for normalizing the gene expression found with qRT-PCR. It is anticipated that these results would improve the selection of suitable reference genes for qRT-PCR assays and lay the foundation for an accurate analysis of gene expression in S. bambusicola.
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Affiliation(s)
- Liang Song
- College of Life Science, Capital Normal University, Beijing, People's Republic of China
| | - Tong Li
- College of Life Science, Capital Normal University, Beijing, People's Republic of China
| | - Li Fan
- College of Life Science, Capital Normal University, Beijing, People's Republic of China
| | - Xiao-Ye Shen
- College of Life Science, Capital Normal University, Beijing, People's Republic of China.
| | - Cheng-Lin Hou
- College of Life Science, Capital Normal University, Beijing, People's Republic of China
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McMillan M, Pereg L. Evaluation of reference genes for gene expression analysis using quantitative RT-PCR in Azospirillum brasilense. PLoS One 2014; 9:e98162. [PMID: 24841066 PMCID: PMC4026395 DOI: 10.1371/journal.pone.0098162] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/29/2014] [Indexed: 11/18/2022] Open
Abstract
Azospirillum brasilense is a nitrogen fixing bacterium that has been shown to have various beneficial effects on plant growth and yield. Under normal conditions A. brasilense exists in a motile flagellated form, which, under starvation or stress conditions, can undergo differentiation into an encapsulated, cyst-like form. Quantitative RT-PCR can be used to analyse changes in gene expression during this differentiation process. The accuracy of quantification of mRNA levels by qRT-PCR relies on the normalisation of data against stably expressed reference genes. No suitable set of reference genes has yet been described for A. brasilense. Here we evaluated the expression of ten candidate reference genes (16S rRNA, gapB, glyA, gyrA, proC, pykA, recA, recF, rpoD, and tpiA) in wild-type and mutant A. brasilense strains under different culture conditions, including conditions that induce differentiation. Analysis with the software programs BestKeeper, NormFinder and GeNorm indicated that gyrA, glyA and recA are the most stably expressed reference genes in A. brasilense. The results also suggested that the use of two reference genes (gyrA and glyA) is sufficient for effective normalisation of qRT-PCR data.
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Affiliation(s)
- Mary McMillan
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
| | - Lily Pereg
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
- * E-mail:
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14
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Fillat MF. The FUR (ferric uptake regulator) superfamily: diversity and versatility of key transcriptional regulators. Arch Biochem Biophys 2014; 546:41-52. [PMID: 24513162 DOI: 10.1016/j.abb.2014.01.029] [Citation(s) in RCA: 212] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/27/2014] [Accepted: 01/31/2014] [Indexed: 11/17/2022]
Abstract
Control of metal homeostasis is essential for life in all kingdoms. In most prokaryotic organisms the FUR (ferric uptake regulator) family of transcriptional regulators is involved in the regulation of iron and zinc metabolism through control by Fur and Zur proteins. A third member of this family, the peroxide-stress response PerR, is present in most Gram-positives, establishing a tight functional interaction with the global regulator Fur. These proteins play a pivotal role for microbial survival under adverse conditions and in the expression of virulence in most pathogens. In this paper we present the current state of the art in the knowledge of the FUR family, including those members only present in more reduced numbers of bacteria, namely Mur, Nur and Irr. The huge amount of work done in the two last decades shows that FUR proteins present considerable diversity in their regulatory mechanisms and interesting structural differences. However, much work needs to be done to obtain a more complete picture of this family, especially in connection with the roles of some members as gas and redox sensors as well as to fully characterize their participation in bacterial adaptative responses.
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Affiliation(s)
- María F Fillat
- Department of Biochemistry and Molecular and Cell Biology, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Pedro Cerbuna, 12, 50009 Zaragoza, Spain.
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González A, Angarica VE, Sancho J, Fillat MF. The FurA regulon in Anabaena sp. PCC 7120: in silico prediction and experimental validation of novel target genes. Nucleic Acids Res 2014; 42:4833-46. [PMID: 24503250 PMCID: PMC4005646 DOI: 10.1093/nar/gku123] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In the filamentous cyanobacterium Anabaena sp. PCC 7120, the ferric uptake regulator FurA functions as a global transcriptional regulator. Despite several analyses have focused on elucidating the FurA-regulatory network, the number of target genes described for this essential transcription factor is limited to a handful of examples. In this article, we combine an in silico genome-wide predictive approach with experimental determinations to better define the FurA regulon. Predicted FurA-binding sites were identified upstream of 215 genes belonging to diverse functional categories including iron homeostasis, photosynthesis and respiration, heterocyst differentiation, oxidative stress defence and light-dependent signal transduction mechanisms, among others. The probabilistic model proved to be effective at discerning FurA boxes from non-cognate sequences, while subsequent electrophoretic mobility shift assay experiments confirmed the in vitro specific binding of FurA to at least 20 selected predicted targets. Gene-expression analyses further supported the dual role of FurA as transcriptional modulator that can act both as repressor and as activator. In either role, the in vitro affinity of the protein to its target sequences is strongly dependent on metal co-regulator and reducing conditions, suggesting that FurA couples in vivo iron homeostasis and the response to oxidative stress to major physiological processes in cyanobacteria.
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Affiliation(s)
- Andrés González
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain and Unidad Asociada BIFI-IQFR (CSIC), 28006 Madrid, Spain
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