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Jroundi F, Povedano-Priego C, Pinel-Cabello M, Descostes M, Grizard P, Purevsan B, Merroun ML. Evidence of microbial activity in a uranium roll-front deposit: Unlocking their potential role as bioenhancers of the ore genesis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160636. [PMID: 36464038 DOI: 10.1016/j.scitotenv.2022.160636] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Uranium (U) roll-front deposits constitute a valuable source for an economical extraction by in situ recovery (ISR) mining. Such technology may induce changes in the subsurface microbiota, raising questions about the way their activities could build a functional ecosystem in such extreme environments (i.e.: oligotrophy and high SO4 concentration and salinity). Additionally, more information is needed to dissipate the doubts about the microbial role in the genesis of such U orebodies. A U roll-front deposit hosted in an aquifer driven system (in Zoovch Ovoo, Mongolia), intended for mining by acid ISR, was previously explored and showed to be governed by a complex bacterial diversity, linked to the redox zonation and the geochemical conditions. Here for the first time, transcriptional activities of microorganisms living in such U ore deposits are determined and their metabolic capabilities allocated in the three redox-inherited compartments, naturally defined by the roll-front system. Several genes encoding for crucial metabolic pathways demonstrated a strong biological role controlling the subsurface cycling of many elements including nitrate, sulfate, metals and radionuclides (e.g.: uranium), through oxidation-reduction reactions. Interestingly, the discovered transcriptional behaviour gives important insights into the good microbial adaptation to the geochemical conditions and their active contribution to the stabilization of the U ore deposits. Overall, evidences on the importance of these microbial metabolic activities in the aquifer system are discussed that may clarify the doubts on the microbial role in the genesis of low-temperature U roll-front deposits, along the Zoovch Ovoo mine.
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Affiliation(s)
- Fadwa Jroundi
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain.
| | - Cristina Povedano-Priego
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - María Pinel-Cabello
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - Michael Descostes
- ORANO Mining, 125 Avenue de Paris, 92330 Châtillon, France; Centre de Géosciences, MINES ParisTech, PSL University, 35 rue St Honoré, 77300 Fontainebleau, France
| | - Pierre Grizard
- ORANO Mining, 125 Avenue de Paris, 92330 Châtillon, France
| | - Bayaarma Purevsan
- Badrakh Energy LLC, Jamyan Gun Avenue - 9, Sukhbaatar district, 1st khoroo, UB-14240, Mongolia
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
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2
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Zhang W, Zhang X, Su Q, Tang M, Zheng H, Zhou X. Genomic features underlying the evolutionary transitions of Apibacter to honey bee gut symbionts. INSECT SCIENCE 2022; 29:259-275. [PMID: 33811731 DOI: 10.1111/1744-7917.12912] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/20/2021] [Accepted: 02/21/2021] [Indexed: 05/16/2023]
Abstract
The gut bacteria of honey bee recognized as a mutualistic partner with the insect host might have originated from a free-living or parasitic lifestyle. However, little is known about the genomic features underlying this lifestyle transition. Here we compared the genomes of bee gut bacteria Apibacter with their close relatives living in different lifestyles. We found that despite general reduction in the Apibacter genome, genes involved in amino acid synthesis and monosaccharide detoxification were retained, which is putatively beneficial to the host. Interestingly, the microaerobic Apibacter species specifically acquired genes encoding for the nitrate respiration (NAR). These together with nitrate transporter and enzymatic cofactor synthesis genes were found clustered in the genomes. The NAR system is also conserved in the cohabitating bee gut microbe Snodgrassella, although with a different structure. This convergence suggests a key role of respiratory nitrate reduction for microaerophilic microbiomes to colonize bee gut epithelium. Genes involved in lipid, histidine degradation were found partially or completely lost in Apibacter. Particularly, genes encoding for the conversion to the toxic intermediates in phenylacetate degradation, as well as other potential virulence factors, are specifically lost in Apibacter group. Antibiotic resistance genes are only sporadically distributed among Apibacter species, but are prevalent in their relatives, which may be related to the remotely living feature and less exposure to antibiotics of their bee hosts. Collectively, this study advanced our knowledge of genomic features specialized to bee gut symbionts.
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Affiliation(s)
- Wenjun Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Qinzhi Su
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Min Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
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3
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Schneider C, Groß SJ, Demeshko S, Bontemps S, Meyer F, Werncke CG. Synthesis and characterisation of a very low-coordinate diferrous [2Fe-2S] 0 unit. Chem Commun (Camb) 2021; 57:10751-10754. [PMID: 34585677 DOI: 10.1039/d1cc04196g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Here we present the synthesis of a unique diferrous [2Fe-2S]0 complex with only three-coordinate iron ions via reduction of a four-coordinate diferric [2Fe-2S]2+ complex with concomitant ligand loss. The obtained compounds were thoroughly examined for their properties (e.g. by 57Fe Mössbauer spectroscopy and magnetic susceptibility measurements). Facile cleavage of the [2Fe-2S] rhombus, commonly seen as rather stable, by CS2 is also shown.
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Affiliation(s)
- Christian Schneider
- Chemistry Department, Philipps-University, Hans-Meerwein-Str. 4, 35043 Marburg, Germany.
| | - Sophie J Groß
- University of Göttingen, Institute of Inorganic Chemistry, Tammannstr. 4, D-37077 Göttingen, Germany
| | - Serhiy Demeshko
- University of Göttingen, Institute of Inorganic Chemistry, Tammannstr. 4, D-37077 Göttingen, Germany
| | - Sébastien Bontemps
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, 31077 Toulouse, France.,Université de Toulouse, UPS, INPT, 31077 Toulouse, France
| | - Franc Meyer
- University of Göttingen, Institute of Inorganic Chemistry, Tammannstr. 4, D-37077 Göttingen, Germany
| | - C Gunnar Werncke
- Chemistry Department, Philipps-University, Hans-Meerwein-Str. 4, 35043 Marburg, Germany.
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Insights into the Structure of Rubisco from Dinoflagellates-In Silico Studies. Int J Mol Sci 2021; 22:ijms22168524. [PMID: 34445230 PMCID: PMC8395205 DOI: 10.3390/ijms22168524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 02/06/2023] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is one of the best studied enzymes. It is crucial for photosynthesis, and thus for all of biosphere’s productivity. There are four isoforms of this enzyme, differing by amino acid sequence composition and quaternary structure. However, there is still a group of organisms, dinoflagellates, single-cell eukaryotes, that are confirmed to possess Rubisco, but no successful purification of the enzyme of such origin, and hence a generation of a crystal structure was reported to date. Here, we are using in silico tools to generate the possible structure of Rubisco from a dinoflagellate representative, Symbiodinium sp. We selected two templates: Rubisco from Rhodospirillum rubrum and Rhodopseudomonas palustris. Both enzymes are the so-called form II Rubiscos, but the first is exclusively a homodimer, while the second one forms homo-hexamers. Obtained models show no differences in amino acids crucial for Rubisco activity. The variation was found at two closely located inserts in the C-terminal domain, of which one extends a helix and the other forms a loop. These inserts most probably do not play a direct role in the enzyme’s activity, but may be responsible for interaction with an unknown protein partner, possibly a regulator or a chaperone. Analysis of the possible oligomerization interface indicated that Symbiodinium sp. Rubisco most likely forms a trimer of homodimers, not just a homodimer. This hypothesis was empowered by calculation of binding energies. Additionally, we found that the protein of study is significantly richer in cysteine residues, which may be the cause for its activity loss shortly after cell lysis. Furthermore, we evaluated the influence of the loop insert, identified exclusively in the Symbiodinium sp. protein, on the functionality of the recombinantly expressed R. rubrum Rubisco. All these findings shed new light onto dinoflagellate Rubisco and may help in future obtainment of a native, active enzyme.
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Singhal N, Sharma A, Kumari S, Garg A, Rai R, Singh N, Kumar M, Goel M. Biophysical and Biochemical Characterization of Nascent Polypeptide-Associated Complex of Picrophilus torridus and Elucidation of Its Interacting Partners. Front Microbiol 2020; 11:915. [PMID: 32528429 PMCID: PMC7264160 DOI: 10.3389/fmicb.2020.00915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/17/2020] [Indexed: 12/15/2022] Open
Affiliation(s)
- Neelja Singhal
- Department of Biophysics, University of Delhi, New Delhi, India
| | - Archana Sharma
- Department of Biophysics, University of Delhi, New Delhi, India
| | - Shobha Kumari
- Department of Biophysics, University of Delhi, New Delhi, India
| | - Anjali Garg
- Department of Biophysics, University of Delhi, New Delhi, India
| | - Ruchica Rai
- Department of Biophysics, University of Delhi, New Delhi, India
| | - Nirpendra Singh
- Regional Centre for Biotechnology, NCR-Biotech Science Cluster, Faridabad, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi, New Delhi, India
| | - Manisha Goel
- Department of Biophysics, University of Delhi, New Delhi, India
- *Correspondence: Manisha Goel,
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Bashiri G, Grove TL, Hegde SS, Lagautriere T, Gerfen GJ, Almo SC, Squire CJ, Blanchard JS, Baker EN. The active site of the Mycobacterium tuberculosis branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase contains a 2Fe-2S cluster. J Biol Chem 2019; 294:13158-13170. [PMID: 31315931 DOI: 10.1074/jbc.ra119.009498] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/15/2019] [Indexed: 01/17/2023] Open
Abstract
Iron-sulfur clusters are protein cofactors with an ancient evolutionary origin. These clusters are best known for their roles in redox proteins such as ferredoxins, but some iron-sulfur clusters have nonredox roles in the active sites of enzymes. Such clusters are often prone to oxidative degradation, making the enzymes difficult to characterize. Here we report a structural and functional characterization of dihydroxyacid dehydratase (DHAD) from Mycobacterium tuberculosis (Mtb), an essential enzyme in the biosynthesis of branched-chain amino acids. Conducting this analysis under fully anaerobic conditions, we solved the DHAD crystal structure, at 1.88 Å resolution, revealing a 2Fe-2S cluster in which one iron ligand is a potentially exchangeable water molecule or hydroxide. UV and EPR spectroscopy both suggested that the substrate binds directly to the cluster or very close to it. Kinetic analysis implicated two ionizable groups in the catalytic mechanism, which we postulate to be Ser-491 and the iron-bound water/hydroxide. Site-directed mutagenesis showed that Ser-491 is essential for activity, and substrate docking indicated that this residue is perfectly placed for proton abstraction. We found that a bound Mg2+ ion 6.5 Å from the 2Fe-2S cluster plays a key role in substrate binding. We also identified a putative entry channel that enables access to the cluster and show that Mtb-DHAD is inhibited by a recently discovered herbicide, aspterric acid, that, given the essentiality of DHAD for Mtb survival, is a potential lead compound for the design of novel anti-TB drugs.
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Affiliation(s)
- Ghader Bashiri
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Subray S Hegde
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Thomas Lagautriere
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Gary J Gerfen
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Christopher J Squire
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - John S Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Edward N Baker
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
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7
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Stegmaier K, Blinn CM, Bechtel DF, Greth C, Auerbach H, Müller CS, Jakob V, Reijerse EJ, Netz DJA, Schünemann V, Pierik AJ. Apd1 and Aim32 Are Prototypes of Bishistidinyl-Coordinated Non-Rieske [2Fe–2S] Proteins. J Am Chem Soc 2019; 141:5753-5765. [DOI: 10.1021/jacs.8b13274] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Edward J. Reijerse
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D45470 Mülheim an der Ruhr, Germany
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8
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He HY, Henderson AC, Du YL, Ryan KS. Two-Enzyme Pathway Links l-Arginine to Nitric Oxide in N-Nitroso Biosynthesis. J Am Chem Soc 2019; 141:4026-4033. [DOI: 10.1021/jacs.8b13049] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hai-Yan He
- Department of Chemistry, University of British Columbia, Vancouver, Canada
| | | | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
| | - Katherine S. Ryan
- Department of Chemistry, University of British Columbia, Vancouver, Canada
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9
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Basile LA, Zalguizuri A, Briones G, Lepek VC. Two Rieske Fe/S Proteins and TAT System in Mesorhizobium loti MAFF303099: Differential Regulation and Roles on Nodulation. FRONTIERS IN PLANT SCIENCE 2018; 9:1686. [PMID: 30515183 PMCID: PMC6256036 DOI: 10.3389/fpls.2018.01686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Mesorhizobium loti MAFF303099 is a rhizobial strain that nodulates Lotus spp. A M. loti MAFF303099 mutant strain affected in the tatC gene was generated. This strain presented an altered protein secretion level to the culture supernatant and also a higher sensitivity to SDS. Its nodulation phenotype on Lotus showed the induction of small and colorless nodules, and in a larger number than those induced by the wild-type strain. In addition, these nodules presented defects in the degree of occupation by rhizobia. Two Rieske Fe/S proteins, encoded by the mll2707 and mlr0970 genes, were predicted as potential Tat substrates in M. loti MAFF303099. The transcriptional expression of mll2707 and mlr0970 genes was analyzed under different oxygen growth conditions. The mll2707 gene was expressed constitutively, while the expression of the mlr0970 gene was only detected under anaerobic and microaerophilic in vitro conditions. Both genes were down-regulated in the tatC mutant strain. mll2707 and mlr0970 mRNAs from the wild-type strain were detected in nodules. Using a translational reporter peptide fusion, we found that the Mll2707 protein was only detectable in the wild-type strain. On the other hand, although Mlr0970 protein was detected in wild-type and tatC mutant strains, its association with the membrane was favored in the wild-type strain. The tatC and the mll2707 mutant strains were affected in the cytochrome c oxidase activity. These results confirm that Mll2707 is required for cytochrome c-dependent respiration and that Tat functionality is required for the correct activity of Mll2707. The mll2707 mutant strain showed a nodulation phenotype similar to the tatC mutant strain, although it presented only a slight difference in comparison with wild-type strain in terms of nodule occupation. No defective phenotype was observed in the nodulation with the mlr0970 mutant strain. These results indicate that, of the two Rieske Fe/S proteins coded by M. loti MAFF303099, only Mll2707 expression is required for the induction of effective nodules, and that the functionality of the Tat system is necessary not only for the correct function of this protein, but also for some other protein required in an earlier stage of the nodulation process.
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10
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Koppel N, Bisanz JE, Pandelia ME, Turnbaugh PJ, Balskus EP. Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins. eLife 2018; 7:33953. [PMID: 29761785 PMCID: PMC5953540 DOI: 10.7554/elife.33953] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/11/2018] [Indexed: 12/21/2022] Open
Abstract
Although the human gut microbiome plays a prominent role in xenobiotic transformation, most of the genes and enzymes responsible for this metabolism are unknown. Recently, we linked the two-gene 'cardiac glycoside reductase' (cgr) operon encoded by the gut Actinobacterium Eggerthella lenta to inactivation of the cardiac medication and plant natural product digoxin. Here, we compared the genomes of 25 E. lenta strains and close relatives, revealing an expanded 8-gene cgr-associated gene cluster present in all digoxin metabolizers and absent in non-metabolizers. Using heterologous expression and in vitro biochemical characterization, we discovered that a single flavin- and [4Fe-4S] cluster-dependent reductase, Cgr2, is sufficient for digoxin inactivation. Unexpectedly, Cgr2 displayed strict specificity for digoxin and other cardenolides. Quantification of cgr2 in gut microbiomes revealed that this gene is widespread and conserved in the human population. Together, these results demonstrate that human-associated gut bacteria maintain specialized enzymes that protect against ingested plant toxins.
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Affiliation(s)
- Nitzan Koppel
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Jordan E Bisanz
- Department of Microbiology & Immunology, University of California, San Francisco, United States
| | | | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, United States.,Chan Zuckerberg Biohub, San Francisco, United States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States.,Broad Institute, Cambridge, United States
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11
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Kublanov IV, Sigalova OM, Gavrilov SN, Lebedinsky AV, Rinke C, Kovaleva O, Chernyh NA, Ivanova N, Daum C, Reddy TBK, Klenk HP, Spring S, Göker M, Reva ON, Miroshnichenko ML, Kyrpides NC, Woyke T, Gelfand MS, Bonch-Osmolovskaya EA. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. Front Microbiol 2017; 8:195. [PMID: 28265262 PMCID: PMC5317091 DOI: 10.3389/fmicb.2017.00195] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 01/26/2017] [Indexed: 11/13/2022] Open
Abstract
The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.
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Affiliation(s)
- Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Olga M Sigalova
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Sergey N Gavrilov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Alexander V Lebedinsky
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia QLD, Australia
| | - Olga Kovaleva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Nikolai A Chernyh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | | | - Chris Daum
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | | | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Oleg N Reva
- Center for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria Pretoria, South Africa
| | - Margarita L Miroshnichenko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut CreekCA, USA; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, BerkeleyCA, USA
| | - Mikhail S Gelfand
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of SciencesMoscow, Russia; Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State UniversityMoscow, Russia; Skolkovo Institute of Science and TechnologyMoscow, Russia; Faculty of Computer Science, National Research University - Higher School of EconomicsMoscow, Russia
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12
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Veit S, Takeda K, Tsunoyama Y, Baymann F, Nevo R, Reich Z, Rögner M, Miki K, Rexroth S. Structural and functional characterisation of the cyanobacterial PetC3 Rieske protein family. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1879-1891. [DOI: 10.1016/j.bbabio.2016.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/12/2016] [Accepted: 09/17/2016] [Indexed: 11/30/2022]
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13
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The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part III. {[Fe2S2](Cys)3(X)} (X=Asp, Arg, His) and {[Fe2S2](Cys)2(His)2} proteins. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Abstract
Twin-arginine protein translocation systems (Tat) translocate fully folded and co-factor-containing proteins across biological membranes. In this review, we focus on the Tat pathway of Gram-positive bacteria. The minimal Tat pathway is composed of two components, namely a TatA and TatC pair, which are often complemented with additional TatA-like proteins. We provide overviews of our current understanding of Tat pathway composition and mechanistic aspects related to Tat-dependent cargo protein translocation. This includes Tat pathway flexibility, requirements for the correct folding and incorporation of co-factors in cargo proteins and the functions of known cargo proteins. Tat pathways of several Gram-positive bacteria are discussed in detail, with emphasis on the Tat pathway of Bacillus subtilis. We discuss both shared and unique features of the different Gram-positive bacterial Tat pathways. Lastly, we highlight topics for future research on Tat, including the development of this protein transport pathway for the biotechnological secretion of high-value proteins and its potential applicability as an antimicrobial drug target in pathogens.
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Affiliation(s)
- Vivianne J Goosens
- MRC Centre for Molecular Bacteriology and Infection, Section of Microbiology, Imperial College London, London, SW7 2AZ, UK
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700, RB, Groningen, The Netherlands.
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15
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Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum. J Bacteriol 2015; 197:2517-35. [PMID: 25986905 DOI: 10.1128/jb.00176-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/12/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Signal transduction is an essential process that allows bacteria to sense their complex and ever-changing environment and adapt accordingly. Three distinct major types of signal-transducing proteins (STPs) can be distinguished: one-component systems (1CSs), two-component systems (2CSs), and extracytoplasmic-function σ factors (ECFs). Since Actinobacteria are particularly rich in STPs, we comprehensively investigated the abundance and diversity of STPs encoded in 119 actinobacterial genomes, based on the data stored in the Microbial Signal Transduction (MiST) database. Overall, we observed an approximately linear correlation between the genome size and the total number of encoded STPs. About half of all membrane-anchored 1CSs are protein kinases. For both 1CSs and 2CSs, a detailed analysis of the domain architectures identified novel proteins that are found only in actinobacterial genomes. Many actinobacterial genomes are particularly enriched for ECFs. As a result of this study, almost 500 previously unclassified ECFs could be classified into 18 new ECF groups. This comprehensive survey demonstrates that actinobacterial genomes encode previously unknown STPs, which may represent new mechanisms of signal transduction and regulation. This information not only expands our knowledge of the diversity of bacterial signal transduction but also provides clear and testable hypotheses about their mechanisms, which can serve as starting points for experimental studies. IMPORTANCE In the wake of the genomic era, with its enormous increase in the amount of available sequence information, the challenge has now shifted toward making sense and use of this treasure chest. Such analyses are a prerequisite to provide meaningful information that can help guide subsequent experimental efforts, such as mechanistic studies on novel signaling strategies. This work provides a comprehensive analysis of signal transduction proteins from 119 actinobacterial genomes. We identify, classify, and describe numerous novel and conserved signaling devices. Hence, our work serves as an important resource for any researcher interested in signal transduction of this important bacterial phylum, which contains organisms of ecological, biotechnological, and medical relevance.
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Taguchi F, Inoue Y, Suzuki T, Inagaki Y, Yamamoto M, Toyoda K, Noutoshi Y, Shiraishi T, Ichinose Y. Characterization of quorum sensing-controlled transcriptional regulator MarR and Rieske (2Fe-2S) cluster-containing protein (Orf5), which are involved in resistance to environmental stresses in Pseudomonas syringae pv. tabaci 6605. MOLECULAR PLANT PATHOLOGY 2015; 16:376-87. [PMID: 25155081 PMCID: PMC6638344 DOI: 10.1111/mpp.12187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Pseudomonas syringae pv. tabaci 6605 (Pta6605) produces acyl homoserine lactones (AHLs), quorum sensing (QS) molecules that are indispensable for virulence in host tobacco infection. Genome-wide transcriptional profiling of several QS-defective mutants revealed that the expression of the genes encoding the MarR family transcriptional regulator (MarR) and a Rieske 2Fe-2S cluster-containing protein (Orf5) located adjacent to psyI, a gene encoding AHL synthetase, are significantly repressed. Exogenous application of AHL recovered the expression of both marR and orf5 genes in the ΔpsyI mutant, indicating that AHL positively regulates the expression of these genes. To investigate the role of these genes in the virulence of Pta6605, ΔmarR and Δorf5 mutants were generated. Both mutants showed decreased swimming and swarming motilities, decreased survival ability under oxidative and nitrosative stresses and, consequently, reduced virulence on host tobacco plants. Transmission electron micrographs showed that the structure of the cell membranes of ΔmarR and Δorf5 mutants was severely damaged. Furthermore, not only the ratio of dead cells, but also the amount of flagella, extracellular DNA and protein released into the culture supernatant, was significantly increased in both mutants, indicating that the disruption of marR and orf5 genes might induce structural changes in the membrane and cell lysis. Because both mutants showed partly similar expression profiles, both gene products might be involved in the same regulatory cascades that are required for QS-dependent survival under environmentally stressed conditions.
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Affiliation(s)
- Fumiko Taguchi
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
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Wu WK, Panyod S, Ho CT, Kuo CH, Wu MS, Sheen LY. Dietary allicin reduces transformation of L-carnitine to TMAO through impact on gut microbiota. J Funct Foods 2015. [DOI: 10.1016/j.jff.2015.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Abstract
Mitochondria are the energy-producing organelles of our cells and derive from bacterial ancestors that became endosymbionts of microorganisms from a different lineage, together with which they formed eukaryotic cells. For a long time it has remained unclear from which bacteria mitochondria actually evolved, even if these organisms in all likelihood originated from the α lineage of proteobacteria. A recent article (Degli Esposti M, et al. 2014. Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PLoS One 9:e96566) has presented novel evidence indicating that methylotrophic bacteria could be among the closest living relatives of mitochondrial ancestors. Methylotrophs are ubiquitous bacteria that live on single carbon sources such as methanol and methane; in the latter case they are called methanotrophs. In this review, I examine their possible ancestry to mitochondria within a survey of the common features that can be found in the central and terminal bioenergetic systems of proteobacteria and mitochondria. I also discuss previously overlooked information on methanotrophic bacteria, in particular their intracytoplasmic membranes resembling mitochondrial cristae and their capacity of establishing endosymbiotic relationships with invertebrate animals and archaic plants. This information appears to sustain the new idea that mitochondrial ancestors could be related to extant methanotrophic proteobacteria, a possibility that the genomes of methanotrophic endosymbionts will hopefully clarify.
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 549] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Goosens VJ, Monteferrante CG, van Dijl JM. Co-factor insertion and disulfide bond requirements for twin-arginine translocase-dependent export of the Bacillus subtilis Rieske protein QcrA. J Biol Chem 2014; 289:13124-31. [PMID: 24652282 DOI: 10.1074/jbc.m113.529677] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The twin-arginine translocation (Tat) pathway can transport folded and co-factor-containing cargo proteins over bacterial cytoplasmic membranes. Functional Tat machinery components, a folded state of the cargo protein and correct co-factor insertion in the cargo protein are generally considered as prerequisites for successful translocation. The present studies were aimed at a dissection of these requirements with regard to the Rieske iron-sulfur protein QcrA of Bacillus subtilis. Notably, QcrA is a component of the cytochrome bc1 complex, which is conserved from bacteria to man. Single amino acid substitutions were introduced into the Rieske domain of QcrA to prevent either co-factor binding or disulfide bond formation. Both types of mutations precluded QcrA translocation. Importantly, a proofreading hierarchy was uncovered, where a QcrA mutant defective in disulfide bonding was quickly degraded, whereas mutant QcrA proteins defective in co-factor binding accumulated in the cytoplasm and membrane. Altogether, these are the first studies on Tat-dependent protein translocation where both oxidative folding and co-factor attachment have been addressed in a single native molecule.
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Affiliation(s)
- Vivianne J Goosens
- From the Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB, Groningen, The Netherlands
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Goosens VJ, Monteferrante CG, van Dijl JM. The Tat system of Gram-positive bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1698-706. [PMID: 24140208 DOI: 10.1016/j.bbamcr.2013.10.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Revised: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 10/26/2022]
Abstract
The twin-arginine protein translocation (Tat) system has a unique ability to translocate folded and co-factor-containing proteins across lipid bilayers. The Tat pathway is present in bacteria, archaea and in the thylakoid membranes of chloroplasts and, depending on the organism and environmental conditions, it can be deemed important for cell survival, virulence or bioproduction. This review provides an overview of the current understanding of the Tat system with specific focus on Gram-positive bacteria. The 'universal minimal Tat system' is composed of a TatA and a TatC protein. However, this pathway is more commonly composed of two TatA-like proteins and one TatC protein. Often the TatA-like proteins have diverged to have two different functions and, in this case, the second TatA-like protein is usually referred to as TatB. The correct folding and/or incorporation of co-factors are requirements for translocation, and the known quality control mechanisms are examined in this review. A number of examples of crosstalk between the Tat system and other protein transport systems, such as the Sec-YidC translocon and signal peptidases or sheddases are also discussed. Further, an overview of specific Gram-positive bacterial Tat systems found in monoderm and diderm species is detailed. Altogether, this review highlights the unique features of Gram-positive bacterial Tat systems and pinpoints key questions that remain to be addressed in future research. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Vivianne J Goosens
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB Groningen, The Netherlands
| | - Carmine G Monteferrante
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB Groningen, The Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB Groningen, The Netherlands.
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Okutan E, Deng L, Mirlashari S, Uldahl K, Halim M, Liu C, Garrett RA, She Q, Peng X. Novel insights into gene regulation of the rudivirus SIRV2 infecting Sulfolobus cells. RNA Biol 2013; 10:875-85. [PMID: 23584138 DOI: 10.4161/rna.24537] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Microarray analysis of infection by a lytic Sulfolobus rudivirus, SIRV2, revealed both the temporal expression of viral genes and the differential regulation of host genes. A highly susceptible strain derived from Sulfolobus solfataricus P2 with a large genomic deletion spanning CRISPR clusters A to D was infected with SIRV2, and subjected to a microarray analysis. Transcripts from a few viral genes were detected at 15 min post-infection and all except one were expressed within 2 h. The earliest expressed genes were located mainly at the termini of the linear viral genome while later expressed genes were concentrated in the central region. Timing of the expression correlated with the known or predicted functions of the viral gene products and, thus, should facilitate functional characterization of many hypothetical viral genes. Evaluation of the microarray data with quantitative reverse-transcription PCR analyses of a few selected viral genes revealed a good correlation between the two methods. Expression of about 3,000 host genes was examined. Seventy-two were downregulated>2-fold that were mainly associated with stress response and vesicle formation, as well as chromosome structure maintenance, which appears to contribute to host chromosome degradation and cellular collapse. A further 76 host genes were upregulated>2-fold and they were dominated by genes associated with metabolism and membrane transport, including phosphate transport and DNA precursor synthesis. The altered transcriptional patterns suggest that the virus reprograms the host cellular machinery to facilitate its own DNA replication and to inhibit cellular processes required for defense against viruses.
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Affiliation(s)
- Ebru Okutan
- Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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23
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Veit S, Takeda K, Tsunoyama Y, Rexroth D, Rögner M, Miki K. Structure of a thermophilic cyanobacterial b6f-type Rieske protein. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1400-8. [PMID: 22993094 DOI: 10.1107/s0907444912034129] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 07/31/2012] [Indexed: 11/10/2022]
Abstract
The `Rieske protein' PetC is one of the key subunits of the cytochrome b(6)f complex. Its Rieske-type [2Fe-2S] cluster participates in the photosynthetic electron-transport chain. Overexpression and careful structure analysis at 2.0 Å resolution of the extrinsic soluble domain of PetC from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 enabled in-depth spectroscopic and structural characterization and suggested novel structural features. In particular, both the protein structure and the positions of the internal water molecules unexpectedly showed a higher similarity to eukaryotic PetCs than to other prokaryotic PetCs. The structure also revealed a deep pocket on the PetC surface which is oriented towards the membrane surface in the whole complex. Its surface properties suggest a binding site for a hydrophobic compound and the complete conservation of the pocket-forming residues in all known PetC sequences indicates the functional importance of this pocket in the cytochrome b(6)f complex.
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Affiliation(s)
- Sebastian Veit
- Plant Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
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Li H, Zhang Q, Li S, Zhu Y, Zhang G, Zhang H, Tian X, Zhang S, Ju J, Zhang C. Identification and characterization of xiamycin A and oxiamycin gene cluster reveals an oxidative cyclization strategy tailoring indolosesquiterpene biosynthesis. J Am Chem Soc 2012; 134:8996-9005. [PMID: 22591327 DOI: 10.1021/ja303004g] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Xiamycin A (XMA) and oxiamycin (OXM) are bacterial indolosesquiterpenes featuring rare pentacyclic ring systems and are isolated from a marine-derived Streptomyces sp. SCSIO 02999. The putative biosynthetic gene cluster for XMA/OXM was identified by a partial genome sequencing approach. Eighteen genes were proposed to be involved in XMA/OXM biosynthesis, including five genes for terpene synthesis via a non-mevalonate pathway, eight genes encoding oxidoreductases, and five genes for regulation and resistance. Targeted disruptions of 13 genes within the xia gene cluster were carried out to probe their encoded functions in XMA/OXM biosynthesis. The disruption of xiaK, encoding an aromatic ring hydroxylase, led to a mutant producing indosespene and a minor amount of XMA. Feeding of indosespene to XMA/OXM nonproducing mutants revealed indosespene as a common precursor for XMA/OXM biosynthesis. Most notably, the flavin dependent oxygenase XiaI was biochemically characterized in vitro to convert indosespene to XMA, revealing an unusual oxidative cyclization strategy tailoring indolosesquiterpene biosynthesis.
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Affiliation(s)
- Huixian Li
- CAS Key Laboratory of Marine Bio-resources Sustainable Utilization, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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25
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Bernát G, Schreiber U, Sendtko E, Stadnichuk IN, Rexroth S, Rögner M, Koenig F. Unique properties vs. common themes: the atypical cyanobacterium Gloeobacter violaceus PCC 7421 is capable of state transitions and blue-light-induced fluorescence quenching. PLANT & CELL PHYSIOLOGY 2012; 53:528-542. [PMID: 22302714 DOI: 10.1093/pcp/pcs009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The atypical unicellular cyanobacterium Gloeobacter violaceus PCC 7421, which diverged very early during the evolution of cyanobacteria, can be regarded as a key organism for understanding many structural, functional, regulatory and evolutionary aspects of oxygenic photosynthesis. In the present work, the performance of two basic photosynthetic adaptation/protection mechanisms, common to all other oxygenic photoautrophs, had been challenged in this ancient cyanobacterium which lacks thylakoid membranes: state transitions and non-photochemical fluorescence quenching. Both low temperature fluorescence spectra and room temperature fluorescence transients show that G. violaceus is capable of performing state transitions similar to evolutionarily more recent cyanobacteria, being in state 2 in darkness and in state 1 upon illumination by weak blue or far-red light. Compared with state 2, variable fluorescence yield in state 1 is strongly enhanced (almost 80%), while the functional absorption cross-section of PSII is only increased by 8%. In contrast to weak blue light, which enhances fluorescence yield via state 1 formation, strong blue light reversibly quenches Chl fluorescence in G. violaceus. This strongly suggests regulated heat dissipation which is triggered by the orange carotenoid protein whose presence was directly proven by immunoblotting and mass spectrometry in this primordial cyanobacterium. The results are discussed in the framework of cyanobacterial evolution.
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Affiliation(s)
- Gábor Bernát
- Plant Biochemistry, Ruhr-University Bochum, D-44801 Bochum, Germany.
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26
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Kallas T. Cytochrome b 6 f Complex at the Heart of Energy Transduction and Redox Signaling. PHOTOSYNTHESIS 2012. [DOI: 10.1007/978-94-007-1579-0_21] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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27
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Chakraborty J, Dutta TK. From lipid transport to oxygenation of aromatic compounds: evolution within the Bet v1-like superfamily. J Biomol Struct Dyn 2011; 29:67-78. [PMID: 21696226 DOI: 10.1080/07391102.2011.10507375] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In absence of significant sequence similarity, remote homology between proteins can be confused with analogy and in such a case, shared ancestry can be inferred in light of certain unique and common features. In the present study, to understand the evolutionary origin of catalytic domain of large subunit of ring-hydroxylating oxygenases (RHOs), belonging to the Bet v1-like superfamily, structure-based phylogenies have been derived from structural alignment of representative proteins of the superfamily. A careful inspection of the structural relatedness of RHOs with the rest of the families showed closest similarity between RHO catalytic domain and PA1206-like protein. In addition, phylogenetic relationship of the Rieske domain of the large subunit of RHOs with functionally and structurally similar proteins has also been elucidated so as to postulate the most possible events leading to the genesis of the large subunit of RHOs.
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Affiliation(s)
- Joydeep Chakraborty
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VII M, Kolkata 700054, India
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28
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Dynamics of the cyanobacterial photosynthetic network: Communication and modification of membrane protein complexes. Eur J Cell Biol 2010; 89:974-82. [DOI: 10.1016/j.ejcb.2010.08.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Characterization of two cytochrome b 6 proteins from the cyanobacterium Gloeobacter violaceus PCC 7421. J Bioenerg Biomembr 2010; 42:517-26. [DOI: 10.1007/s10863-010-9279-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 01/22/2010] [Indexed: 11/29/2022]
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Tsunoyama Y, Bernát G, Dyczmons NG, Schneider D, Rögner M. Multiple Rieske proteins enable short- and long-term light adaptation of Synechocystis sp. PCC 6803. J Biol Chem 2009; 284:27875-27883. [PMID: 19674969 PMCID: PMC2788838 DOI: 10.1074/jbc.m109.011189] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 08/12/2009] [Indexed: 11/06/2022] Open
Abstract
In contrast to eukaryotes, most cyanobacteria contain several isoforms of the Rieske iron-sulfur protein, PetC, resulting in heterogeneity in the composition of the cytochrome b(6)f complexes. Of three isoforms in the mesophilic cyanobacterium Synechocystis PCC 6803, PetC1 is the major Rieske protein in the cytochrome b(6)f complex, whereas the physiological function of PetC2 and PetC3 is still uncertain. Comparison of wild type and various petC-deficient strains under selected light conditions revealed distinct functional differences: high-light exposure of wild type cells resulted in a significantly enhanced petC2 transcript level, whereas a Delta petC1 mutant showed a low cytochrome b(6)f content, low electron flux, and a considerably increased accumulation of cytochrome-bd oxidase. In contrast to wild type and Delta petC1, Delta petC2 and Delta petC3 strains still grew fast under high-light conditions although all three Rieske proteins are required for maximal electron transport rates. Although the presence of PetC3 appears to be required for activation of the cyclic electron transport, state transitions were more effective in the absence of PetC2 and/or PetC3. In summary, our data suggest defined roles of the various PetC proteins in short- and long-term light adaptation.
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Affiliation(s)
- Yuichi Tsunoyama
- Department of Plant Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany; Division of Biology, Radioisotope Research Center, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Gábor Bernát
- Department of Plant Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Nina G Dyczmons
- Department of Plant Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Dirk Schneider
- Department of Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Matthias Rögner
- Department of Plant Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany.
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Simmons JM, Müller TA, Hausinger RP. Fe(II)/alpha-ketoglutarate hydroxylases involved in nucleobase, nucleoside, nucleotide, and chromatin metabolism. Dalton Trans 2008:5132-42. [PMID: 18813363 PMCID: PMC2907160 DOI: 10.1039/b803512a] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fe(II)/alpha-ketoglutarate-dependent hydroxylases uniformly possess a double-stranded beta-helix fold with two conserved histidines and one carboxylate coordinating their mononuclear ferrous ions. Oxidative decomposition of the alpha-keto acid is proposed to generate a ferryl-oxo intermediate capable of hydroxylating unactivated carbon atoms in a myriad of substrates. This Perspective focuses on a subgroup of these enzymes that are involved in pyrimidine salvage, purine decomposition, nucleoside and nucleotide hydroxylation, DNA/RNA repair, and chromatin modification. The varied reaction schemes are presented, and selected structural and kinetic information is summarized.
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Affiliation(s)
- Jana M. Simmons
- Department of Biochemistry and Molecular Biology, 6193 Biomedical Physical Sciences Bldg, Michigan State University, East Lansing, Michigan, USA, 48824-4320
| | - Tina A. Müller
- Department of Microbiology and Molecular Genetics, 6193 Biomedical Physical Sciences Bldg, Michigan State University, East Lansing, Michigan, USA, 48824-4320
| | - Robert P. Hausinger
- Department of Biochemistry and Molecular Biology, 6193 Biomedical Physical Sciences Bldg, Michigan State University, East Lansing, Michigan, USA, 48824-4320
- Department of Microbiology and Molecular Genetics, 6193 Biomedical Physical Sciences Bldg, Michigan State University, East Lansing, Michigan, USA, 48824-4320
- Quantitative Biology Program, 6193 Biomedical Physical Sciences Bldg, Michigan State University, East Lansing, Michigan, USA, 48824-4320
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Iida Y, Kurata T, Harimoto Y, Tsuge T. Nitrite reductase gene upregulated during conidiation is involved in macroconidium formation in Fusarium oxysporum. PHYTOPATHOLOGY 2008; 98:1099-1106. [PMID: 18943456 DOI: 10.1094/phyto-98-10-1099] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Fusarium oxysporum produces three kinds of asexual spores, microconidia, macroconidia, and chlamydospores. We previously found that the transcript level of the nitrite reductase gene of F. oxysporum, named FoNIIA, was markedly upregulated during conidiation compared with during vegetative growth. FoNIIA was also found to be positively regulated by Ren1 that is a transcription regulator controlling development of microconidia and macroconidia. In this study, we analyzed the function of FoNIIA in conidiation of F. oxysporum. Conidiation cultures showed markedly higher level of accumulation of FoNiiA protein as well as FoNIIA mRNA than vegetative growth cultures. FoNIIA protein was significantly decreased in cultures of the REN1 disruption mutant compared with that of the wild type. These results confirmed that FoNIIA expression is upregulated during conidiation and is positively regulated by REN1. The FoNIIA disruption mutants produced microconidia, macroconidia, and chlamydospores, which were morphologically indistinguishable from those of the wild type. The mutants, however, produced significantly fewer macroconidia than the wild type, although the wild type and mutant strains produced similar numbers of microconidia and chlamydospores. These results demonstrate that nitrite reductase is involved in quantitative control of macroconidium formation as well as nitrate utilization in F. oxysporum.
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Affiliation(s)
- Y Iida
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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Aldridge C, Spence E, Kirkilionis MA, Frigerio L, Robinson C. Tat-dependent targeting of Rieske iron-sulphur proteins to both the plasma and thylakoid membranes in the cyanobacterium Synechocystis PCC6803. Mol Microbiol 2008; 70:140-50. [PMID: 18699865 DOI: 10.1111/j.1365-2958.2008.06401.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cyanobacteria possess a differentiated membrane system and transport proteins into both the periplasm and thylakoid lumen. We have used green fluorescent protein (GFP)-tagged constructs to study the Tat protein transporter and Rieske Tat substrates in Synechocystis PCC6803. The Tat system has been shown to operate in the plasma membrane; we show here that it is also relatively abundant in the thylakoid membrane network, indicating that newly synthesized Tat substrates are targeted to both membrane systems. Synechocystis contains three Rieske iron-sulphur proteins, all of which contain typical twin-arginine signal-like sequences at their N-termini. We show that two of these proteins (PetC1 and PetC2) are obligate Tat substrates when expressed in Escherichia coli. The Rieske proteins exhibit differential localization in Synechocystis 6803; PetC1 and PetC2 are located in the thylakoid membrane, while PetC3 is primarily targeted to the plasma membrane. The combined data show that Tat substrates are directed with high precision to both membrane systems in this cyanobacterium, raising the question of how, and when, intracellular sorting to the correct membrane is achieved.
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Affiliation(s)
- Cassie Aldridge
- Department of Biological Sciences, University of Warwick, Coventry, UK
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Orio M, Mouesca JM. Variation of average g values and effective exchange coupling constants among [2Fe-2S] clusters: a density functional theory study of the impact of localization (trapping forces) versus delocalization (double-exchange) as competing factors. Inorg Chem 2008; 47:5394-416. [PMID: 18491857 DOI: 10.1021/ic701730h] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A phenomenological model aimed at rationalizing variations in both average g-tensor values (gav identical with 1/3Sigmaigi ) and effective exchange coupling constants Jeff (defined as two-thirds of the energy difference between the S = 3/2 and S = 1/2 spin states) has been derived in order to describe the great variety of magnetic properties exhibited by reduced [2Fe-2S] clusters in proteins. The key quantity in the present analysis is the ratio Delta E/B computed from two competing terms. Delta Ecomprises various effects that result in trapping-site asymmetries: vibronic coupling and the chemical nature (S/N/O) and conformations of the ligands on the one hand and solvation terms, the hydrogen bonding network, etc., on the other. All of these additive terms (in a "bottom-up" approach) favor valence localization of the reducing electron onto one of the two iron sites. In contrast, the B term is the double-exchange term, which favors electronic delocalization. Both gav and Jeff can be expressed as functions of Delta E/ B. We have also shown that electronic localization generally favors small gav and large Jeff values (while the opposite is true for electronic delocalization) in a comparative study of the spectroscopic features of plant-type ferredoxins (Fd's) and Rieske centers (and related mutants). Two other types of problems were particularly challenging. The first of these involved deprotonated Rieske centers and the xanthine oxidase clusters II, which are characterized by very small Jeff values (40-45 cm (-1) with a J S A. S B model) correlated with unusually large gav values (in the range 1.97-2.01) as a result of an antisymmetric exchange coupling mechanism. The second concerned the analogous Fd's from Clostridium pasteurianum (Cp) and Aquifex aeolicus (Aa). Detailed Mössbauer studies of the C56S mutant of the Cp system revealed a mixture of clusters with valence-localized S = 1/2 and valence-delocalized S = 9/2 ground states. We relied on crystallographic structures of wild-type and mutant Aa Fd's in order to explain such a distribution of spin states.
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Affiliation(s)
- Maylis Orio
- Laboratory of Inorganic and Biological Chemistry, Grenoble cedex, France
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Rupprecht E, Gathmann S, Fuhrmann E, Schneider D. Three different DnaK proteins are functionally expressed in the cyanobacterium Synechocystis sp. PCC 6803. MICROBIOLOGY-SGM 2007; 153:1828-1841. [PMID: 17526840 DOI: 10.1099/mic.0.2007/005876-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Multiple dnaK genes appear to be common in cyanobacteria; the function of the encoded proteins is, however, still elusive. To characterize the dnaK gene family from the cyanobacterium Synechocystis sp. PCC 6803 in detail, genetic analyses were combined with analyses of the expression and localization patterns of the three encoded proteins. While significant expression of all three genes was found, the results obtained clearly indicate physiological differences of the three proteins in vivo, and DnaK2 seems to have a key function in Synechocystis. Expression of DnaK3 appears also to be as essential as expression of DnaK2, whereas the dnaK1 gene was deleted without resulting in any distorted phenotype. In line with a suggested privileged function, expression of DnaK2 altered most significantly after heat shock.
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Affiliation(s)
- Eva Rupprecht
- Fakultät für Biologie, Albert-Ludwigs-Universität, 79104 Freiburg, Germany
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
| | - Sven Gathmann
- Fakultät für Biologie, Albert-Ludwigs-Universität, 79104 Freiburg, Germany
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
| | - Eva Fuhrmann
- Fakultät für Biologie, Albert-Ludwigs-Universität, 79104 Freiburg, Germany
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
| | - Dirk Schneider
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
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Muller D, Médigue C, Koechler S, Barbe V, Barakat M, Talla E, Bonnefoy V, Krin E, Arsène-Ploetze F, Carapito C, Chandler M, Cournoyer B, Cruveiller S, Dossat C, Duval S, Heymann M, Leize E, Lieutaud A, Lièvremont D, Makita Y, Mangenot S, Nitschke W, Ortet P, Perdrial N, Schoepp B, Siguier P, Simeonova DD, Rouy Z, Segurens B, Turlin E, Vallenet D, Dorsselaer AV, Weiss S, Weissenbach J, Lett MC, Danchin A, Bertin PN. A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet 2007; 3:e53. [PMID: 17432936 PMCID: PMC1851979 DOI: 10.1371/journal.pgen.0030053] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Accepted: 02/23/2007] [Indexed: 12/03/2022] Open
Abstract
Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the beta-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth.
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Affiliation(s)
- Daniel Muller
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | | | - Sandrine Koechler
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | | | - Mohamed Barakat
- Laboratoire d'Écologie Microbienne de la Rhizosphère et d'Environnements Extrêmes, UMR6191 CNRS, CEA and Université Aix-Marseille II, Saint-Paul-lez-Durance, France
| | - Emmanuel Talla
- Laboratoire de Chimie Bactérienne, UPR9043 CNRS, Institut de Biologie Structurale et Microbiologie, Marseille, France
| | - Violaine Bonnefoy
- Laboratoire de Chimie Bactérienne, UPR9043 CNRS, Institut de Biologie Structurale et Microbiologie, Marseille, France
| | - Evelyne Krin
- Génétique des Génomes Bactériens, URA2171, Institut Pasteur, Paris, France
| | - Florence Arsène-Ploetze
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique, Institut Pluridisciplinaire Hubert Curien, UMR7178 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Michael Chandler
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100 CNRS, Toulouse, France
| | - Benoît Cournoyer
- Ecologie Microbienne, UMR5557 CNRS and Université Claude Bernard–Lyon 1, Villeurbanne, France
| | | | | | - Simon Duval
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR9036 CNRS, Institut de Biologie Structurale et Microbiologie, Marseille, France
| | - Michael Heymann
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Emmanuelle Leize
- Laboratoire de Spectrométrie de Masse Bio-Organique, Institut Pluridisciplinaire Hubert Curien, UMR7178 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Aurélie Lieutaud
- Laboratoire de Chimie Bactérienne, UPR9043 CNRS, Institut de Biologie Structurale et Microbiologie, Marseille, France
| | - Didier Lièvremont
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Yuko Makita
- Génétique des Génomes Bactériens, URA2171, Institut Pasteur, Paris, France
| | | | - Wolfgang Nitschke
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR9036 CNRS, Institut de Biologie Structurale et Microbiologie, Marseille, France
| | - Philippe Ortet
- Laboratoire d'Écologie Microbienne de la Rhizosphère et d'Environnements Extrêmes, UMR6191 CNRS, CEA and Université Aix-Marseille II, Saint-Paul-lez-Durance, France
| | - Nicolas Perdrial
- Centre de Géochimie de la Surface, UMR7517 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Barbara Schoepp
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR9036 CNRS, Institut de Biologie Structurale et Microbiologie, Marseille, France
| | - Patricia Siguier
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100 CNRS, Toulouse, France
| | - Diliana D Simeonova
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Zoé Rouy
- Génoscope, UMR8030 CNRS, Evry Cedex, France
| | | | - Evelyne Turlin
- Génétique des Génomes Bactériens, URA2171, Institut Pasteur, Paris, France
| | | | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-Organique, Institut Pluridisciplinaire Hubert Curien, UMR7178 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Stéphanie Weiss
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | | | - Marie-Claire Lett
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Antoine Danchin
- Génétique des Génomes Bactériens, URA2171, Institut Pasteur, Paris, France
| | - Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
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Ferrer M, Golyshina OV, Beloqui A, Golyshin PN, Timmis KN. The cellular machinery of Ferroplasma acidiphilum is iron-protein-dominated. Nature 2007; 445:91-4. [PMID: 17203061 DOI: 10.1038/nature05362] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 10/20/2006] [Indexed: 11/09/2022]
Abstract
Ferroplasma is a genus of the Archaea, one of the three branches of the tree of life, and belongs to the order Thermoplasmatales (Euryarchaeota), which contains the most acidophilic microbes yet known. Ferroplasma species live in acid mine drainage, acidic pools and environments containing sulphidic ores such as pyrite and characterized by pH values of 0-2 and high concentrations of ferrous iron and other heavy metals. F. acidiphilum strain Y(T) is a chemoautotroph that grows optimally at pH 1.7 and gains energy by oxidizing ferrous iron and carbon by the fixation of carbon dioxide. Here we show that 86% of 189 investigated cellular proteins of F. acidiphilum are iron-metalloproteins. These include proteins with deduced structural, chaperone and catalytic roles, not described as iron-metalloproteins in any other organism so far investigated. The iron atoms in the proteins seem to organize and stabilize their three-dimensional structures, to act as 'iron rivets'. Analysis of proteins of the phylogenetic neighbour Picrophilus torridus and of the habitat neighbour Acidithiobacillus ferrooxidans revealed far fewer and only typical metalloproteins. F. acidiphilum therefore has a currently unique iron-protein-dominated cellular machinery and biochemical phylogeny.
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Affiliation(s)
- Manuel Ferrer
- CSIC, Institute of Catalysis, Cantoblanco, 28049 Madrid, Spain.
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Schneider D, Volkmer T, Rögner M. PetG and PetN, but not PetL, are essential subunits of the cytochrome b6f complex from Synechocystis PCC 6803. Res Microbiol 2006; 158:45-50. [PMID: 17224258 DOI: 10.1016/j.resmic.2006.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Revised: 08/10/2006] [Accepted: 10/03/2006] [Indexed: 10/23/2022]
Abstract
The cytochrome b(6)f complex consists of four large core subunits and an additional four low molecular weight subunits, the function of which is elusive thus far. Here we sought to determine whether small subunits PetG, PetL, and PetN are essential for a cyanobacterial cytochrome b(6)f complex. We found that only PetL is dispensable, whereas PetG and PetN appear to be essential. Possible roles of the small cytochrome b(6)f complex subunits are discussed, and observations from our study are compared with previous findings.
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Affiliation(s)
- Dirk Schneider
- Institut für Biochemie und Molekularbiologie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
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