1
|
Azkargorta M, Wojtas MN, Abrescia NGA, Elortza F. Lysine methylation mapping of crenarchaeal DNA-directed RNA polymerases by collision-induced and electron-transfer dissociation mass spectrometry. J Proteome Res 2014; 13:2637-48. [PMID: 24625205 DOI: 10.1021/pr500084p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymatic machineries fundamental for information processing (e.g., transcription, replication, translation) in Archaea are simplified versions of their eukaryotic counterparts. This is clearly noticeable in the conservation of sequence and structure of corresponding enzymes (see for example the archaeal DNA-directed RNA polymerase (RNAP)). In Eukarya, post-translational modifications (PTMs) often serve as functional regulatory factors for various enzymes and complexes. Among the various PTMs, methylation and acetylation have been recently attracting most attention. Nevertheless, little is known about such PTMs in Archaea, and cross-methodological studies are scarce. We examined methylation and N-terminal acetylation of endogenously purified crenarchaeal RNA polymerase from Sulfolobus shibatae (Ssh) and Sulfolobus acidocaldarius (Sac). In-gel and in-solution protein digestion methods were combined with collision-induced dissociation (CID) and electron-transfer dissociation (ETD) mass spectrometry analysis. Overall, 20 and 26 methyl-lysines for S. shibatae and S. acidocaldarius were identified, respectively. Furthermore, two N-terminal acetylation sites for each of these organisms were assessed. As a result, we generated a high-confidence data set for the mapping of methylation and acetylation sites in both Sulfolobus species, allowing comparisons with the data previously obtained for RNAP from Sulfolobus solfataricus (Sso). We confirmed that all observed methyl-lysines are on the surface of the RNAP.
Collapse
Affiliation(s)
- Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, ProteoRed-ISCIII, CIBERehd, 48160 Derio, Spain
| | | | | | | |
Collapse
|
2
|
Wojtas MN, Abrescia NGA. Soaking of DNA into crystals of archaeal RNA polymerase achieved by desalting in droplets. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1134-8. [PMID: 22949213 PMCID: PMC3433216 DOI: 10.1107/s1744309112033507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 07/24/2012] [Indexed: 11/06/2023]
Abstract
Transcription is a fundamental process across the three domains of life and is carried out by multi-subunit enzymatic DNA-directed RNA polymerases (RNAPs). The interaction of RNAP with nucleic acids is tightly controlled for precise and processive RNA synthesis. Whilst a wealth of structural information has been gathered on the eukaryotic Pol II in complex with DNA/RNA, no information exists on its ancestral counterpart archaeal RNAP. Thus, in order to extend knowledge of the archaeal transcriptional apparatus, crystallization of Sulfolobus shibatae RNAP (molecular mass of ~400 kDa) with DNA fragments was pursued. To achieve this goal, crystal growth was first optimized using a nanoseeding technique. An ad hoc soaking protocol was then put into place, which consisted of gently exchanging the high-salt buffer used for apo-RNAP crystal growth into a low-salt buffer necessary for DNA binding to RNAP. Of the various crystals screened, one diffracted to 4.3 Å resolution and structural analysis showed the presence of bound DNA [Wojtas et al. (2012). Nucleic Acids Res. 40, doi:10.1093/nar/gks692].
Collapse
Affiliation(s)
| | - Nicola G. A. Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| |
Collapse
|
3
|
Wojtas MN, Mogni M, Millet O, Bell SD, Abrescia NGA. Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA. Nucleic Acids Res 2012; 40:9941-52. [PMID: 22848102 PMCID: PMC3479171 DOI: 10.1093/nar/gks692] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Multi-subunit RNA polymerases (RNAPs) in all three domains of life share a common ancestry. The composition of the archaeal RNAP (aRNAP) is not identical between phyla and species, with subunits Rpo8 and Rpo13 found in restricted subsets of archaea. While Rpo8 has an ortholog, Rpb8, in the nuclear eukaryal RNAPs, Rpo13 lacks clear eukaryal orthologs. Here, we report crystal structures of the DNA-bound and free form of the aRNAP from Sulfolobus shibatae. Together with biochemical and biophysical analyses, these data show that Rpo13 C-terminus binds non-specifically to double-stranded DNA. These interactions map on our RNAP–DNA binary complex on the downstream DNA at the far end of the DNA entry channel. Our findings thus support Rpo13 as a RNAP–DNA stabilization factor, a role reminiscent of eukaryotic general transcriptional factors. The data further yield insight into the mechanisms and evolution of RNAP–DNA interaction.
Collapse
|
4
|
Jun SH, Reichlen MJ, Tajiri M, Murakami KS. Archaeal RNA polymerase and transcription regulation. Crit Rev Biochem Mol Biol 2011; 46:27-40. [PMID: 21250781 DOI: 10.3109/10409238.2010.538662] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
To elucidate the mechanism of transcription by cellular RNA polymerases (RNAPs), high-resolution X-ray crystal structures together with structure-guided biochemical, biophysical, and genetics studies are essential. The recently solved X-ray crystal structures of archaeal RNAP allow a structural comparison of the transcription machinery among all three domains of life. The archaea were once thought of closely related to bacteria, but they are now considered to be more closely related to the eukaryote at the molecular level than bacteria. According to these structures, the archaeal transcription apparatus, which includes RNAP and general transcription factors (GTFs), is similar to the eukaryotic transcription machinery. Yet, the transcription regulators, activators and repressors, encoded by archaeal genomes are closely related to bacterial factors. Therefore, archaeal transcription appears to possess an intriguing hybrid of eukaryotic-type transcription apparatus and bacterial-like regulatory mechanisms. Elucidating the transcription mechanism in archaea, which possesses a combination of bacterial and eukaryotic transcription mechanisms that are commonly regarded as separate and mutually exclusive, can provide data that will bring basic transcription mechanisms across all life forms.
Collapse
Affiliation(s)
- Sung-Hoon Jun
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | | | | | | |
Collapse
|
5
|
Korkhin Y, Unligil UM, Littlefield O, Nelson PJ, Stuart DI, Sigler PB, Bell SD, Abrescia NGA. Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure. PLoS Biol 2009; 7:e1000102. [PMID: 19419240 PMCID: PMC2675907 DOI: 10.1371/journal.pbio.1000102] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 03/19/2009] [Indexed: 11/19/2022] Open
Abstract
The archaeal RNA polymerase (RNAP) shares structural similarities with eukaryotic RNAP II but requires a reduced subset of general transcription factors for promoter-dependent initiation. To deepen our knowledge of cellular transcription, we have determined the structure of the 13-subunit DNA-directed RNAP from Sulfolobus shibatae at 3.35 Å resolution. The structure contains the full complement of subunits, including RpoG/Rpb8 and the equivalent of the clamp-head and jaw domains of the eukaryotic Rpb1. Furthermore, we have identified subunit Rpo13, an RNAP component in the order Sulfolobales, which contains a helix-turn-helix motif that interacts with the RpoH/Rpb5 and RpoA'/Rpb1 subunits. Its location and topology suggest a role in the formation of the transcription bubble.
Collapse
Affiliation(s)
- Yakov Korkhin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, United States of America
| | - Ulug M Unligil
- Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, United States of America
| | - Otis Littlefield
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, United States of America
| | - Pamlea J Nelson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, United States of America
| | - David I Stuart
- Division of Structural Biology and the Oxford Protein Production Facility, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Paul B Sigler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, United States of America
| | - Stephen D Bell
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Nicola G. A Abrescia
- Division of Structural Biology and the Oxford Protein Production Facility, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Structural Biology Unit, CIC bioGUNE, Derio, Spain
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
6
|
Archaeal transcription: function of an alternative transcription factor B from Pyrococcus furiosus. J Bacteriol 2007; 190:157-67. [PMID: 17965161 DOI: 10.1128/jb.01498-07] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of the hyperthermophile archaeon Pyrococcus furiosus encodes two transcription factor B (TFB) paralogs, one of which (TFB1) was previously characterized in transcription initiation. The second TFB (TFB2) is unusual in that it lacks recognizable homology to the archaeal TFB/eukaryotic TFIIB B-finger motif. TFB2 functions poorly in promoter-dependent transcription initiation, but photochemical cross-linking experiments indicated that the orientation and occupancy of transcription complexes formed with TFB2 at the strong gdh promoter are similar to the orientation and occupancy of transcription complexes formed with TFB1. Initiation complexes formed by TFB2 display a promoter opening defect that can be bypassed with a preformed transcription bubble, suggesting a mechanism to explain the low TFB2 transcription activity. Domain swaps between TFB1 and TFB2 showed that the low activity of TFB2 is determined mainly by its N terminus. The low activity of TFB2 in promoter opening and transcription can be partially relieved by transcription factor E (TFE). The results indicate that the TFB N-terminal region, containing conserved Zn ribbon and B-finger motifs, is important in promoter opening and that TFE can compensate for defects in the N terminus through enhancement of promoter opening.
Collapse
|
7
|
Dixit V, Bini E, Drozda M, Blum P. Mercury inactivates transcription and the generalized transcription factor TFB in the archaeon Sulfolobus solfataricus. Antimicrob Agents Chemother 2004; 48:1993-9. [PMID: 15155190 PMCID: PMC415588 DOI: 10.1128/aac.48.6.1993-1999.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2003] [Revised: 12/16/2003] [Accepted: 02/19/2004] [Indexed: 11/20/2022] Open
Abstract
Mercury has a long history as an antimicrobial agent effective against eukaryotic and prokaryotic organisms. Despite its prolonged use, the basis for mercury toxicity in prokaryotes is not well understood. Archaea, like bacteria, are prokaryotes but they use a simplified version of the eukaryotic transcription apparatus. This study examined the mechanism of mercury toxicity to the archaeal prokaryote Sulfolobus solfataricus. In vivo challenge with mercuric chloride instantaneously blocked cell division, eliciting a cytostatic response at submicromolar concentrations and a cytocidal response at micromolar concentrations. The cytostatic response was accompanied by a 70% reduction in bulk RNA synthesis and elevated rates of degradation of several transcripts, including tfb-1, tfb-2, and lacS. Whole-cell extracts prepared from mercuric chloride-treated cells or from cell extracts treated in vitro failed to support in vitro transcription of 16S rRNAp and lacSp promoters. Extract-mixing experiments with treated and untreated extracts excluded the occurrence of negative-acting factors in the mercury-treated cell extracts. Addition of transcription factor B (TFB), a general transcription factor homolog of eukaryotic TFIIB, to mercury-treated cell extracts restored >50% of in vitro transcription activity. Consistent with this finding, mercuric ion treatment of TFB in vitro inactivated its ability to restore the in vitro transcription activity of TFB-immunodepleted cell extracts. These findings indicate that the toxicity of mercuric ion in S. solfataricus is in part the consequence of transcription inhibition due to TFB-1 inactivation.
Collapse
MESH Headings
- Animals
- Archaeal Proteins/genetics
- Archaeal Proteins/immunology
- Blotting, Northern
- Colony Count, Microbial
- DNA, Bacterial/drug effects
- DNA, Bacterial/genetics
- Mercury/toxicity
- Mice
- RNA, Bacterial/analysis
- RNA, Bacterial/biosynthesis
- RNA, Messenger/analysis
- RNA, Messenger/biosynthesis
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/biosynthesis
- Recombinant Proteins/genetics
- Sulfolobus/drug effects
- Sulfolobus/genetics
- Sulfolobus/growth & development
- Transcription Factor TFIIB/genetics
- Transcription Factor TFIIB/immunology
- Transcription, Genetic/drug effects
Collapse
Affiliation(s)
- Vidula Dixit
- George Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0666, USA
| | | | | | | |
Collapse
|
8
|
Richard DJ, Bell SD, White MF. Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase. Nucleic Acids Res 2004; 32:1065-74. [PMID: 14872062 PMCID: PMC373395 DOI: 10.1093/nar/gkh259] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Archaeal transcription utilizes a complex multisubunit RNA polymerase and the basal transcription factors TBP and TF(II)B, closely resembling its eukaryal counterpart. We have uncovered a tight physical and functional interaction between RNA polymerase and the single-stranded DNA-binding protein SSB in Sulfolobus solfataricus. SSB stimulates transcription from promoters in vitro under TBP-limiting conditions and supports transcription in the absence of TBP. SSB also rescues transcription from repression by reconstituted chromatin. We demonstrate the potential for promoter melting by SSB, suggesting a plausible basis for the stimulation of transcription. This stimulation requires both the single-stranded DNA-binding domain and the acidic C-terminal tail of the SSB. The tail forms a stable interaction with RNA polymerase. These data reveal an unexpected role for single-stranded DNA-binding proteins in transcription in archaea.
Collapse
Affiliation(s)
- Derek J Richard
- Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | | | | |
Collapse
|
9
|
Worthington P, Blum P, Perez-Pomares F, Elthon T. Large-scale cultivation of acidophilic hyperthermophiles for recovery of secreted proteins. Appl Environ Microbiol 2003; 69:252-7. [PMID: 12514002 PMCID: PMC152466 DOI: 10.1128/aem.69.1.252-257.2003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An electric water heater was modified for large-scale cultivation of aerobic acidophilic hyperthermophiles to enable recovery of secreted proteins. Critical changes included thermostat replacement, redesign of the temperature control circuit, and removal of the cathodic anticorrosion system. These alterations provided accurate temperature and pH control. The bioreactor was used to cultivate selected strains of the archaeon Sulfolobus solfataricus and other species within this genus. Reformulation of a basal salts medium facilitated preparation of large culture volumes and eliminated sterilization-induced precipitation of medium components. Substrate induction of synthesis of the S. solfataricus-secreted alpha-amylase during growth in a defined medium supported the utility of the bioreactor for studies of physiologically regulated processes. An improved purification strategy was developed by using strong cation-exchange chromatography for recovery of the alpha-amylase and the processing of large sample volumes of acidic culture supernatant. These findings should simplify efforts to study acidophilic hyperthermophilic microbes and their secreted proteins.
Collapse
Affiliation(s)
- Penny Worthington
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | | | | | | |
Collapse
|