Expanded target and cofactor repertoire for the transcriptional activator LysM from Sulfolobus

Song, Ningning; Duc, Trong Nguyen; Oeffelen, Liesbeth Van; Peeters, Eveline; Charlier, Daniël

doi:10.1093/nar/gkt021

Cited by 22 publications

(32 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We compared the Ss-LrpB binding profile to the locations of the LysM binding regions mapped previously [16] and observed a significant overlap: 29 of the 37 Ss-LrpB binding regions were also associated with LysM (Figure 6A; Table 1). Of note, no cross-reactivity of Ss-LrpB- and LysM-specific nanobodies with other Lrp-type proteins has ever been observed [16, 35].…”

Section: Resultsmentioning

confidence: 87%

“…Furthermore, a significant fraction of binding regions is located at a significant distance from the nearest TSS and associated promoter and/or is even intragenic, an observation made for bacterial [46–49] and for archaeal TFs as well [16, 50]. The newly discovered genomic targets that contain a binding motif are generally contacted by Ss-LrpB through non-cooperative low-affinity binding, in contrast to the local gene targets.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, it has been observed and/or predicted by sequence analyses that a subset of archaeal Lrp-like TFs do not interact with amino acids, in contrast to most other archaeal Lrp-like TFs [10–16] and to bacterial Lrp-like regulators that invariably bind amino acids. Known archaeal Lrp-like TFs have regulon sizes ranging from one or a few targets to a large number of genes and operons.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The genome-wide binding profile of the Sulfolobus solfataricustranscription factor Ss-LrpB shows binding events beyond direct transcription regulation

et al. 2013

Self Cite

View full text Add to dashboard Cite

BackgroundGene regulatory processes are largely resulting from binding of transcription factors to specific genomic targets. Leucine-responsive Regulatory Protein (Lrp) is a prevalent transcription factor family in prokaryotes, however, little information is available on biological functions of these proteins in archaea. Here, we study genome-wide binding of the Lrp-like transcription factor Ss-LrpB from Sulfolobus solfataricus.ResultsChromatin immunoprecipitation in combination with DNA microarray analysis (ChIP-chip) has revealed that Ss-LrpB interacts with 36 additional loci besides the four previously identified local targets. Only a subset of the newly identified binding targets, concentrated in a highly variable IS-dense genomic region, is also bound in vitro by pure Ss-LrpB. There is no clear relationship between the in vitro measured DNA-binding specificity of Ss-LrpB and the in vivo association suggesting a limited permissivity of the crenarchaeal chromatin for transcription factor binding. Of 37 identified binding regions, 29 are co-bound by LysM, another Lrp-like transcription factor in S. solfataricus. Comparative gene expression analysis in an Ss-lrpB mutant strain shows no significant Ss-LrpB-mediated regulation for most targeted genes, with exception of the CRISPR B cluster, which is activated by Ss-LrpB through binding to a specific motif in the leader region.ConclusionsThe genome-wide binding profile presented here implies that Ss-LrpB is associated at additional genomic binding sites besides the local gene targets, but acts as a specific transcription regulator in the tested growth conditions. Moreover, we have provided evidence that two Lrp-like transcription factors in S. solfataricus, Ss-LrpB and LysM, interact in vivo.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-828) contains supplementary material, which is available to authorized users.

show abstract

Section: Resultsmentioning

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The genome-wide binding profile of the Sulfolobus solfataricustranscription factor Ss-LrpB shows binding events beyond direct transcription regulation

et al. 2013

Self Cite

View full text Add to dashboard Cite

show abstract

“…DNA fragments were purified using MiniElute columns (Qiagen) and quantified using the Qubit dsDNA HS kit (Life Technologies). PCR and qPCR were performed to determine the DNA species and the enrichment by Mmp -aCPSF1 or Mmp -aRpoL as described previously 58, 60 . For PCR amplification, 1 μL each of input and IP or mock-IP DNA sample was used in a 25 μl reaction mix containing 400 nM of the corresponding oligonucleotide primer (Supplementary Table 2).…”

Section: Methodsmentioning

confidence: 99%

aCPSF1 controlled archaeal transcription termination: a prototypical eukaryotic model

Zhang

et al. 2019

Preprint

View full text Add to dashboard Cite

21Transcription termination defines RNA 3′-ends and guarantees programmed 22 transcriptomes, thus is an essential biological process for life. However, transcription 23 termination mechanisms remain almost unknown in Archaea. Here reported the first 24 general transcription termination factor of Archaea, the conserved ribonuclease aCPSF1, 25 and elucidated its 3′-end cleavage dependent termination mechanism. Depletion of 26 Mmp-aCPSF1 in a methanoarchaeon Methanococcus maripaludis caused a genome-27 wide transcription termination defect and overall transcriptome chaos, and cold-28 sensitive growth. Transcript-3′end-sequencing (Term-seq) revealed transcriptions 29 mostly terminated downstream of a uridine-rich terminator motif, where Mmp-aCPSF1 30 performed cleavage. The endoribonuclease activity was determined essential to 31 terminate transcription in vivo as well. Through super-resolution photoactivated 32 localization microscopy imaging, co-immunoprecipitation, and chromatin 33 immunoprecipitation, we demonstrated that Mmp-aCPSF1 localizes within nucleoid 34 and associates with RNAP and chromosomes. aCPSF1 appears to co-evolve with 35 archaeal RNAPs, and two distant orthologs each from Lokiarchaeota and 36Thaumarchaeota could replace Mmp-aCPSF1 to termination transcription. Thus, 37 aCPSF1 dependent termination mechanism could be universally employed in Archaea, 38 including Lokiarchaeota, one supposed archaeal ancestor of Eukaryotes. Therefore, the 39 reported aCPSF1 cleavage-dependent termination mode not only hints an archetype of 40 Eukaryotic 3′-end processing/cleavage triggered RNAP II termination, but also would 41 3 shed lights on understanding the complex eukaryotic termination based on the 42 simplified archaeal model. 43 44 4 Introduction 45 Transcription, the fundamental biological process in transforming genetic information 46 from DNA to proteins, must be properly terminated 1-3 . Transcription termination 47 functions in i) defining RNA 3′-ends, ii) preventing read-through resulted inappropriate 48 expression of downstream genes or antisense transcriptions, iii) recycling RNA 49 polymerase (RNAP), and iv) minimizing biomacromolecular machinery collision 2-4 . 50 Consequently, organisms have evolved precise mechanisms to govern transcription 51 termination 2-5 . Bacteria primarily employ Rho-dependent and -independent (intrinsic) 52 termination mechanisms. The former relies on an RNA translocase, Rho, to dissociate 53 the transcription elongation complex (TEC), while the latter depends merely on nascent 54 RNA structures harboring 7-8 base-paired hairpins followed by adjacent uridine 55 residues 2,3,6,7 . In Eukaryotes, RNAP II, which transcribes mRNAs and non-coding 56 RNAs, employs multifaceted termination strategies by an involvement of transcript 3′-57 end processing event; the poly(A) sites, one 3′-end processing/termination signal, are 58 recognized by a cleavage and polyadenylation complex (CPF/CPSF), in which the 59 endoribonuclease, human CPSF73 or yeast Ysh1, cleaves RNA downst...

show abstract

“…As such, accurate position weight matrices [5] and cooperative binding constants [11] could be determined, which can further be used to predict genomic binding sites.…”

Section: Introductionmentioning

confidence: 99%

The ‘Densitometric Image Analysis Software’ and Its Application to Determine Stepwise Equilibrium Constants from Electrophoretic Mobility Shift Assays

et al. 2014

Self Cite

View full text Add to dashboard Cite

Current software applications for densitometric analysis, such as ImageJ, QuantityOne (BioRad) and the Intelligent or Advanced Quantifier (Bio Image) do not allow to take the non-linearity of autoradiographic films into account during calibration. As a consequence, quantification of autoradiographs is often regarded as problematic, and phosphorimaging is the preferred alternative. However, the non-linear behaviour of autoradiographs can be described mathematically, so it can be accounted for. Therefore, the ‘Densitometric Image Analysis Software’ has been developed, which allows to quantify electrophoretic bands in autoradiographs, as well as in gels and phosphorimages, while providing optimized band selection support to the user. Moreover, the program can determine protein-DNA binding constants from Electrophoretic Mobility Shift Assays (EMSAs). For this purpose, the software calculates a chosen stepwise equilibrium constant for each migration lane within the EMSA, and estimates the errors due to non-uniformity of the background noise, smear caused by complex dissociation or denaturation of double-stranded DNA, and technical errors such as pipetting inaccuracies. Thereby, the program helps the user to optimize experimental parameters and to choose the best lanes for estimating an average equilibrium constant. This process can reduce the inaccuracy of equilibrium constants from the usual factor of 2 to about 20%, which is particularly useful when determining position weight matrices and cooperative binding constants to predict genomic binding sites. The MATLAB source code, platform-dependent software and installation instructions are available via the website http://micr.vub.ac.be.

show abstract

Expanded target and cofactor repertoire for the transcriptional activator LysM from Sulfolobus

Cited by 22 publications

References 58 publications

The genome-wide binding profile of the Sulfolobus solfataricustranscription factor Ss-LrpB shows binding events beyond direct transcription regulation

The genome-wide binding profile of the Sulfolobus solfataricustranscription factor Ss-LrpB shows binding events beyond direct transcription regulation

aCPSF1 controlled archaeal transcription termination: a prototypical eukaryotic model

The ‘Densitometric Image Analysis Software’ and Its Application to Determine Stepwise Equilibrium Constants from Electrophoretic Mobility Shift Assays

Contact Info

Product

Resources

About