Biology subjects

Winkelman, J. T.

Publications and source records attributed to Winkelman, J. T..

6 recordsLinked to original sources

bioRxiv2025

Swarm-seq Reveals Functional Divergence in CsrA Homologs Across Bacteria.

Bacteria employ sophisticated post-transcriptional regulatory mechanisms to adapt to environmental changes. Carbon storage regulator A (CsrA), a highly conserved small RNA-binding protein, serves as a critical post-transcriptional regulator by recognizing GGA motifs in target transcripts and typically repressing translation. Despite extensive research, how this conserved regulator has evolved diverse species-specific regulatory networks remains unclear. Here, using Bacillus subtilis as an experimental chassis, we have developed Swarm-seq -- a high-throughput functional genomics platform capable of assessing CsrA homologs across the Bacterial domain for their ability to regulate flagella-dependent swarming motility. Systematically testing over five-hundred codon-optimized csrA homologs for flagellin (Hag) repression revealed striking functional divergence, i.e., broadly two classes of CsrAs. Class I, exemplified by CsrAHp from Helicobacter pylori and RsmN from Pseudomonas aeruginosa strongly inhibited swarming, while Class II, exemplified by CsrAEc from Escherichia coli and RsmA from P. aeruginosa failed despite high sequence conservation. This differential activity occurred despite all proteins targeting identical GGA motifs in the hag transcripts 5UTR, indicating evolutionary plasticity in RNA-binding specificity beyond motif recognition. We propose that this plasticity enables a conserved global regulator to develop species-specific regulons through subtle structural adaptations, facilitating diverse physiological responses across bacterial taxa. Our findings establish B. subtilis as a powerful platform for characterizing CsrA homologs from genetically intractable bacteria, providing insights into post-transcriptional regulatory network evolution.

microbiology↗

bioRxiv2022

Combinatorial control of biofilm development by quorum-sensing and nutrient-sensing regulators.

The human pathogen Pseudomonas aeruginosa, a leading cause of hospital-acquired infections, inhabits and forms sessile antibiotic-resistant communities called biofilms in a wide range of biotic and abiotic environments. In this study, we examined how two global sensory signaling pathways - the RhlR quorum-sensing system and the CbrA/CbrB nutritional adaptation system - intersect to control biofilm development. Previous work has shown that individually these two systems repress biofilm formation. Here, we used biofilm analyses, RNA-seq, and reporter assays to explore the combined effect of information flow through RhlR and CbrA on biofilm development. We find that the {Delta}rhlR{Delta}cbrA double mutant exhibits a biofilm morphology and an associated transcriptional response distinct from wildtype and the parent {Delta}rhlR and {Delta}cbrA mutants indicating codominance of each signaling pathway. The {Delta}rhlR{Delta}cbrA mutant rapidly gains suppressor mutations that map to the carbon catabolite repression protein Crc. The combined absence of RhlR and CbrA leads to drastic reduction in the abundance of the Crc antagonist small RNA CrcZ. Thus, CrcZ acts as the molecular convergence point for quorum- and nutrient-sensing cues. Furthermore, in the absence of antagonism by CrcZ, Crc promotes the expression of biofilm matrix components - Pel exopolysaccharide, and CupB and CupC fimbriae. Therefore, this study uncovers a regulatory link between nutritional adaption and quorum sensing with potential implications for anti-biofilm targeting strategies. AUTHOR SUMMARYBacterial pathogens often form multicellular communities encased in an extra cytoplasmic matrix called biofilms as a virulence strategy. Biofilm development is controlled by various environmental stimuli that are decoded and converted into appropriate cellular responses. How information from two or more stimuli is integrated is poorly understood. Using Pseudomonas aeruginosa biofilm formation as a model, we studied the intersection of two global sensory signaling pathways - quorum sensing and nutritional adaptation. We find parallel regulation by each pathway that converges on the abundance of a small RNA. Thus, we describe a regulatory link between P. aeruginosa quorum-sensing and nutritional adaptation pathways that allows integration of information from each system into the control of biofilm development. These results expand our understanding of the genetic regulatory strategies that allow P. aeruginosa to successfully colonize host during chronic infections.

microbiology↗

bioRxiv2022

Structural and mechanistic basis of σ-dependent transcriptional pausing

In {sigma}-dependent transcriptional pausing, the transcription initiation factor {sigma}, translocating with RNA polymerase (RNAP), makes sequence-specific protein-DNA interactions with a promoter-like sequence element in the transcribed region, inducing pausing. It has been proposed that, in {sigma}-dependent pausing, the RNAP active center can access off-pathway "backtracked" states that are substrates for the transcript-cleavage factors of the Gre family, and on-pathway "scrunched" states that mediate pause escape. Here, using site-specific protein-DNA photocrosslinking to define positions of the RNAP trailing and leading edges and of {sigma} relative to DNA at the{lambda} PR promoter, we show directly that {sigma}-dependent pausing in the absence of GreB in vitro predominantly involves a state backtracked by 2-4 bp, and that {sigma}-dependent pausing in the presence of GreB in vitro and in vivo predominantly involves a state scrunched by 2-3 bp. Analogous experiments with a library of 47 ([~]16,000) transcribed-region sequences show that the state scrunched by 2-3 bp--and only that state--is associated with the consensus sequence, T-3N-2Y-1G+1, (where -1 corresponds to the position of the RNA 3 end), which is identical to the consensus for pausing in initial transcription, and which is related to the consensus for pausing in transcription elongation. Experiments with heteroduplex templates show that sequence information at position T-3 resides in the DNA nontemplate strand. A cryo-EM structure of a complex engaged in {sigma}-dependent pausing reveals positions of DNA scrunching on the DNA nontemplate and template strands and suggests that position T-3 of the consensus sequence exerts its effects by facilitating scrunching.

biochemistry↗

bioRxiv2021

Structural and mechanistic basis of RNA extension in reiterative transcription initiation: RNA slippingwithout DNA scrunching

Reiterative transcription initiation, observed at promoters that contain homopolymeric sequences at the transcription start site, generates RNA products having 5 sequences non-complementary to the DNA template. Here, using crystallography and cryo-EM to define structures, protein-DNA-photocrosslinking to map positions of RNAP leading and trailing edges relative to DNA, and single-molecule DNA nanomanipulation to assess RNAP-dependent DNA unwinding, we show that RNA extension in reiterative transcription initiation: (1) occurs without DNA scrunching, (2) involves a short, 2-3 bp RNA-DNA hybrid, and (3) generates RNA that exits RNAP through the portal by which scrunched nontemplate-strand DNA exits RNAP in standard transcription initiation. The results establish that, whereas RNA extension in standard transcription initiation proceeds through a scrunching mechanism, RNA extension in reiterative transcription initiation proceeds through a slippage mechanism, with slipping of RNA relative to DNA within a short RNA-DNA hybrid, and with extrusion of RNA from RNAP through an alternative RNA exit.

molecular biology↗

bioRxiv2021

Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

Chemical modifications of RNA 5' ends enable "epitranscriptomic" regulation, influencing multiple aspects of RNA fate. In transcription initiation, a large inventory of substrates compete with nucleoside triphosphates (NTPs) for use as initiating entities, providing an ab initio mechanism for altering the RNA 5' end. In Escherichia coli cells, RNAs with a 5'-end hydroxyl are generated by use of dinucleotide RNAs as primers for transcription initiation, "primer-dependent initiation." Here we use massively systematic transcript end readout ("MASTER") to detect and quantify RNA 5' ends generated by primer-dependent initiation for ~410 (~1,000,000) promoter sequences in E. coli. The results show primer-dependent initiation in E. coli involves any of the 16 possible dinucleotide primers and depends on promoter sequences in, upstream, and downstream of the primer binding site. The results yield a consensus sequence for primer-dependent initiation, YTSS-2NTSS-1NTSSWTSS+1, where TSS is the transcription start site, NTSS-1NTSS is the primer binding site, Y is pyrimidine, and W is A or T. Biochemical and structure-determination studies show that the base pair (nontemplate-strand base:template-strand base) immediately upstream of the primer binding site (Y:RTSS-2, where R is purine) exerts its effect through the base on the DNA template strand (RTSS-2) through inter-chain base stacking with the RNA primer. Results from analysis of a large set of natural, chromosomally-encoded E. coli promoters support the conclusions from MASTER. Our findings provide a mechanistic and structural description of how TSS-region sequence hard-codes not only the TSS position, but also the potential for epitranscriptomic regulation through primer-dependent transcription initiation.

biochemistry↗

bioRxiv2019

XACT-seq comprehensively defines the promoter-position and promoter-sequence determinants for initial-transcription pausing

Pausing by RNA polymerase (RNAP) during transcription elongation, in which a translocating RNAP uses a "stepping" mechanism, has been studied extensively, but pausing by RNAP during initial transcription, in which a promoter-anchored RNAP uses a "scrunching" mechanism, has not. We report a method that directly defines RNAP-active-center position relative to DNA in vivo with single-nucleotide resolution (XACT-seq; crosslink-between-active-center-and-template sequencing). We apply this method to detect and quantify pausing in initial transcription at 411 ([~]4,000,000) promoter sequences in vivo, in Escherichia coli. The results show initial-transcription pausing can occur in each nucleotide addition during initial transcription, particularly the first 4-5 nucleotide additions. The results further show initial-transcription pausing occurs at sequences that resemble the consensus sequence element for transcription-elongation pausing. Our findings define the positional and sequence determinants for initial-transcription pausing and establish initial-transcription pausing is hard-coded by sequence elements similar to those for transcription-elongation pausing.

biochemistry↗