About

Dr. Cari Vanderpool is an adjunct professor of microbiology at the University of Minnesota and is affiliated with the Illinois College of Liberal Arts & Sciences School of Molecular & Cellular Biology. Her research investigates RNA-mediated mechanisms of genetic regulation in bacteria, focusing on how bacteria adjust gene expression in response to environmental stresses to ensure survival and competitiveness. Her lab studies small RNAs (sRNAs), non-coding RNA molecules involved in regulating stress responses through mechanisms such as base pairing with target mRNAs to influence their stability or translation. Her work includes the global discovery and characterization of small RNA regulatory networks, with particular emphasis on sRNA functions in bacterial physiology, metabolism, and structure. Notable contributions involve developing tools like SPOT for sRNA target prediction, elucidating the regulation of carbohydrate transport and metabolism via sRNAs such as SgrS, and exploring sRNA roles in membrane structure and function through lipid modifications regulated by sRNAs like RydC, ArrS, and CpxQ. Additionally, her research extends to prophage-encoded regulators, such as DicF and DicB, which influence bacterial cell division and metabolism, and to the regulation of gut microbes, especially within the phylum Bacteroidetes. Her work aims to deepen understanding of bacterial gene regulation mechanisms, with implications for microbial physiology and host interactions.

Research topics

• Biology
• Genetics
• Cell biology
• Computational biology
• Microbiology
• Biochemistry

Selected publications

• Small RNAs positively and negatively control transcription elongation through modulation of Rho utilization site accessibility

  mBio · 2025-10-31 · 1 citations

  articleOpen accessSenior author

  ABSTRACT Bacteria use a multi-layered regulatory strategy to precisely and rapidly tune gene expression in response to environmental cues. Small RNAs (sRNAs) form an important layer of gene expression control and most act post-transcriptionally to control translation and stability of mRNAs. We have shown that at least five different sRNAs (RydC, CpxQ, ArrS, GcvB, and OxyS) in Escherichia coli regulate the cyclopropane fatty acid synthase ( cfa ) mRNA. These sRNAs bind at different sites in the long 5′ untranslated region (UTR) of cfa mRNA, and previous work suggested that they modulate RNase E-dependent mRNA turnover. Rho-dependent transcription termination in the cfa 5′' UTR was demonstrated, leading us to hypothesize that the sRNAs might also regulate cfa transcription elongation. In this study, we find that a pyrimidine-rich region flanked by sRNA binding sites in the cfa 5′ UTR is required for premature Rho-dependent termination. We discovered that sRNA-dependent regulation of cfa depends on Rho, and the activating sRNA RydC has only a minor effect on RNase E-mediated turnover of cfa mRNA. A stem-loop structure in the cfa 5′ UTR sequesters the pyrimidine-rich region required for Rho-dependent termination. The repressing sRNA CpxQ binds to the 5′ portion of the stem and increases Rho-dependent termination, whereas the activating sRNA RydC binds downstream of the stem and decreases termination. These results reveal the versatile mechanisms sRNAs use to regulate target gene expression at transcriptional and post-transcriptional levels and demonstrate that regulation by sRNAs in long UTRs can involve modulation of transcription elongation. IMPORTANCE Bacteria respond to stress by rapidly regulating gene expression. Regulation can occur through the control of messenger RNA (mRNA) production (transcription elongation), stability of mRNAs, or translation of mRNAs. Bacteria can use small RNAs (sRNAs) to regulate gene expression at each of these steps, but we often do not understand how this works at a molecular level. In this study, we find that sRNAs in Escherichia coli regulate gene expression at the level of transcription elongation by promoting or inhibiting transcription termination by a protein called Rho. These results help us understand new molecular mechanisms of gene expression regulation in bacteria.

  PublisherDOI

• Plasmid transmission dynamics and evolution of partner quality in a natural population of <i>Rhizobium leguminosarum</i>

  mBio · 2025-11-10 · 2 citations

  articleOpen access

  ABSTRACT Many bacterial traits important to host–microbe symbiosis are determined by genes carried on extrachromosomal replicons, such as plasmids, chromids, and integrative and conjugative elements. Multiple such replicons often coexist within a single cell and, due to horizontal mobility, have patterns of variation and evolutionary histories that are distinct from each other and from the bacterial chromosome. In nitrogen-fixing Rhizobium , genes carried on multiple plasmids make up a third of the genome, are necessary for the formation of symbiosis, and underlie bacterial traits, including host plant benefits. Thus, the genomics and transmission of plasmids in Rhizobium underlie the ecology and evolution of this important model symbiont. Here, we leverage a natural population of clover-associated Rhizobium in which partner quality has declined in response to long-term nitrogen fertilization. We use 62 novel, reference-quality genomes to characterize 256 replicons in the plasmidome and study their genomics and transmission patterns. We find that, of the four most frequent plasmid types, two (types II and III) have more stable size, larger core genomes, and track the chromosomal phylogeny (display more vertical transmission), while others (type I and type IV, or symbiosis plasmid, pSym) vary substantially in size and shared gene content and have phylogenies consistent with frequent horizontal transmission. We also find differentiation in pSym subtypes driven by long-term nitrogen fertilization. Our results highlight the variation in plasmid transmission dynamics within a single symbiont and implicate plasmid horizontal transmission in the rapid evolution of partner quality. IMPORTANCE Understanding how bacterial genes move through natural populations is critical for understanding how bacterial traits evolve. Nitrogen-fixing bacteria Rhizobium leguminosarum live in symbiosis with plants and are a model for studying plasmid transmission and how mobile genetic elements impact the evolution of bacteria and plants. Here, we characterize the genomes of a natural bacterial population, then use novel approaches to show that mechanisms of gene transmission vary across multiple plasmid types that coexist within R. leguminosarum cells. We find that changes in the frequency of specific pSym types are associated with the decline of symbiotic partner quality in strains isolated from environments undergoing long-term fertilization. These results underscore the importance of plasmid transmission and evolution in shaping ecosystem processes like nitrogen cycling via bacterial-plant symbiosis. Our study provides a framework for probing plasmid dynamics within natural bacterial populations and how plasmid transmission affects genetic diversity and ecological interactions in bacteria.

  PublisherDOI

• The <i>Salmonella</i> pathogenicity island 1-encoded small RNA InvR mediates post-transcriptional feedback control of the activator HilA in <i>Salmonella</i>

  Journal of Bacteriology · 2025-02-27 · 4 citations

  articleOpen accessSenior author

  ABSTRACT Salmonella Pathogenicity Island 1 (SPI1) encodes a Type-3 secretion system (T3SS) essential for Salmonella invasion of intestinal epithelial cells. Many environmental and regulatory signals control SPI1 gene expression, but in most cases, the molecular mechanisms remain unclear. Many regulatory signals control SPI1 at a post-transcriptional level, and we have identified a number of small RNAs (sRNAs) that control the SPI1 regulatory circuit. The transcriptional regulator HilA activates the expression of the genes encoding the SPI1 T3SS structural and primary effector proteins. Transcription of hilA is controlled by the AraC-like proteins HilD, HilC, and RtsA. The hilA mRNA 5′ untranslated region (UTR) is ~350 nucleotides in length and binds the RNA chaperone Hfq, suggesting it is a likely target for sRNA-mediated regulation. We used rGRIL-seq (reverse global sRNA target identification by ligation and sequencing) to identify sRNAs that bind to the hilA 5′ UTR. The rGRIL-seq data, along with genetic analyses, demonstrate the SPI1-encoded sRNA inv asion gene-associated R NA (InvR) base pairs at a site overlapping the hilA ribosome binding site. HilD and HilC activate both invR and hilA . InvR, in turn, negatively regulates the translation of the hilA mRNA. Thus, the SPI1-encoded sRNA InvR acts as a negative feedback regulator of SPI1 expression. Our results suggest that InvR acts to fine-tune SPI1 expression and prevents overactivation of hilA expression, highlighting the complexity of sRNA regulatory inputs controlling SPI1 and Salmonella virulence. IMPORTANCE Salmonella Typhimurium infections pose a significant public health concern, leading to illnesses that range from mild gastroenteritis to severe systemic infection. Infection requires a complex apparatus that the bacterium uses to invade the intestinal epithelium. Understanding how Salmonella regulates this system is essential for addressing these infections effectively. Here, we show that the small RNA (sRNA) InvR imposes a negative feedback regulation on the expression of the invasion system. This work underscores the role of sRNAs in Salmonella 's complex regulatory network, offering new insights into how these molecules contribute to bacterial adaptation and pathogenesis.

  PublisherDOI

• Transcriptional and post-transcriptional mechanisms modulate cyclopropane fatty acid synthase through small RNAs in <i>Escherichia coli</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-02-12

  preprintOpen accessSenior authorCorresponding

  Abstract The small RNA (sRNA) RydC strongly activates cfa , which encodes the cyclopropane fatty acid synthase. Previous work demonstrated that RydC activation of cfa increases conversion of unsaturated fatty acids to cyclopropanated fatty acids in membrane lipids and changes the biophysical properties of membranes, making cells more resistant to acid stress. The conditions and regulators that control RydC synthesis had not previously been identified. In this study, we demonstrate that RydC regulation of cfa is important for resistance to membrane-disrupting conditions. We identify a GntR-family transcription factor, YieP, that represses rydC transcription and show that YieP indirectly regulates cfa through RydC. YieP positively autoregulates its own transcription. We further identify additional sRNA regulatory inputs that contribute to control of RydC and cfa . The translation of yieP is repressed by the Fnr-dependent sRNA, FnrS, making FnrS an indirect activator of rydC and cfa. Conversely, RydC activity on cfa is antagonized by the OmpR-dependent sRNA OmrB. Altogether, this work illuminates a complex regulatory network involving transcriptional and post-transcriptional inputs that link control of membrane biophysical properties to multiple environmental signals. Importance Bacteria experience many environmental stresses that challenge their membrane integrity. To withstand these challenges, bacteria sense what stress is occurring and mount a response that protects membranes. Previous work documented the important roles of small RNA (sRNA) regulators in membrane stress responses. One sRNA, RydC, helps cells cope with membrane-disrupting stresses by promoting changes in the types of lipids incorporated into membranes. In this study, we identified a regulator, YieP, that controls when RydC is produced, and additional sRNA regulators that modulate YieP levels and RydC activity. These findings illuminate a complex regulatory network that helps bacteria sense and respond to membrane stress.

  PublisherOA PDFDOI

• Determinants of raffinose family oligosaccharide use in <i>Bacteroides</i> species

  Journal of Bacteriology · 2024-09-27 · 1 citations

  articleOpen accessSenior author

  ABSTRACT Bacteroides species are successful colonizers of the human colon and can utilize a wide variety of complex polysaccharides and oligosaccharides that are indigestible by the host. To do this, they use enzymes encoded in polysaccharide utilization loci (PULs). While recent work has uncovered the PULs required for the use of some polysaccharides, how Bacteroides utilize smaller oligosaccharides is less well studied. Raffinose family oligosaccharides (RFOs) are abundant in plants, especially legumes, and consist of variable units of galactose linked by α-1,6 bonds to a sucrose (glucose α-1-β-2 fructose) moiety. Previous work showed that an α-galactosidase, BT1871, is required for RFO utilization in Bacteroides thetaiotaomicron . Here, we identify two different types of mutations that increase BT1871 mRNA levels and improve B. thetaiotaomicron growth on RFOs. First, a novel spontaneous duplication of BT1872 and BT1871 places these genes under the control of a ribosomal promoter, driving high BT1871 transcription. Second, nonsense mutations in a gene encoding the PUL24 anti-sigma factor likewise increase BT1871 transcription. We then show that hydrolases from PUL22 work together with BT1871 to break down the sucrose moiety of RFOs and determine that the master regulator of carbohydrate utilization (BT4338) plays a role in RFO utilization in B. thetaiotaomicron . Examining the genomes of other Bacteroides species, we found homologs of BT1871 in a subset and showed that representative strains of species with a BT1871 homolog grew better on melibiose than species that lack a BT1871 homolog. Altogether, our findings shed light on how an important gut commensal utilizes an abundant dietary oligosaccharide. IMPORTANCE The gut microbiome is important in health and disease. The diverse and densely populated environment of the gut makes competition for resources fierce. Hence, it is important to study the strategies employed by microbes for resource usage. Raffinose family oligosaccharides are abundant in plants and are a major source of nutrition for the microbiota in the colon since they remain undigested by the host. Here, we study how the model commensal organism, Bacteroides thetaiotaomicron utilizes raffinose family oligosaccharides. This work highlights how an important member of the microbiota uses an abundant dietary resource.

  PublisherDOI

• Determinants of raffinose family oligosaccharide use in <i>Bacteroides</i> species

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-06-07 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Bacteroides species are successful colonizers of the human gut and can utilize a wide variety of complex polysaccharides and oligosaccharides that are indigestible by the host. To do this, they use enzymes encoded in Polysaccharide Utilization Loci (PULs). While recent work has uncovered the PULs required for use of some polysaccharides, how Bacteroides utilize smaller oligosaccharides is less well studied. Raffinose family oligosaccharides (RFOs) are abundant in plants, especially legumes, and consist of variable units of galactose linked by ⍺-1,6 bonds to a sucrose (glucose ⍺-1-β-2 fructose) moiety. Previous work showed that an α-galactosidase, BT1871, is required for RFO utilization in Bacteroides thetaiotaomicron . Here, we identify two different types of mutations that increase BT1871 mRNA levels and improve B. thetaiotaomicron growth on RFOs. First, a novel spontaneous duplication of BT1872 and BT1871 places these genes under control of a ribosomal promoter, driving high BT1871 transcription. Second, nonsense mutations in a gene encoding the PUL24 anti-sigma factor likewise increase BT1871 transcription. We then show that hydrolases from PUL22 work together with BT1871 to break down the sucrose moiety of RFOs and determine that the master regulator of carbohydrate utilization (BT4338) plays a role in RFO utilization in B. thetaiotaomicron . Examining the genomes of other Bacteroides species, we found homologs of BT1871 in subset and show that representative strains of species containing a BT1871 homolog grew better on melibiose than species that lack a BT1871 homolog. Altogether, our findings shed light on how an important gut commensal utilizes an abundant dietary oligosaccharide. Importance The gut microbiome is important in health and disease. The diverse and densely populated environment of the gut makes competition for resources fierce. Hence, it is important to study the strategies employed by microbes for resource usage. Raffinose family oligosaccharides are abundant in plants and are a major source of nutrition for the gut microbiota since they remain undigested by the host. Here, we study how the model gut commensal, Bacteroides thetaiotaomicron utilizes raffinose family oligosaccharides. This work highlights how an important member of the microbiota uses an abundant dietary resource.

  PublisherOA PDFDOI

• The <i>Salmonella</i> pathogenicity island 1-encoded small RNA InvR mediates post-transcriptional feedback control of the activator HilA in <i>Salmonella</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-11-22 · 2 citations

  preprintOpen accessSenior authorCorresponding

  ABSTRACT Salmonella Pathogenicity Island 1 (SPI1) encodes a type three secretion system (T3SS) essential for Salmonella invasion of intestinal epithelial cells. Many environmental and regulatory signals control SPI1 gene expression, but in most cases, the molecular mechanisms remain unclear. Many of these regulatory signals control SPI1 at a post-transcriptional level and we have identified a number of small RNAs (sRNAs) that control the SPI1 regulatory circuit. The transcriptional regulator HilA activates expression of the genes encoding the SPI1 T3SS structural and primary effector proteins. Transcription of hilA is controlled by the AraC-like proteins HilD, HilC, and RtsA. The hilA mRNA 5’ untranslated region (UTR) is ~350-nuclotides in length and binds the RNA chaperone Hfq, suggesting it is a likely target for sRNA-mediated regulation. We used the rGRIL-seq (reverse global sRNA target identification by ligation and sequencing) method to identify sRNAs that bind to the hilA 5’ UTR. The rGRIL-seq data, along with genetic analyses, demonstrate that the SPI1-encoded sRNA InvR base pairs at a site overlapping the hilA ribosome binding site. HilD and HilC activate both invR and hilA . InvR in turn negatively regulates the translation of the hilA mRNA. Thus, the SPI1-encoded sRNA InvR acts as a negative feedback regulator of SPI1 expression. Our results suggest that InvR acts to fine-tune SPI1 expression and prevent overactivation of hilA expression, highlighting the complexity of sRNA regulatory inputs controlling SPI1 and Salmonella virulence. IMPORTANCE Salmonella Typhimurium infections pose a significant public health concern, leading to illnesses that range from mild gastroenteritis to severe systemic infection. Infection is initiated and requires a complex apparatus that the bacterium uses to invade the intestinal epithelium. Understanding how Salmonella regulates this system is essential for addressing these infections effectively. Here we show that the small RNA (sRNA) InvR imposes negative feedback regulation on expression of the invasion system. This work underscores the role of sRNAs in Salmonella’s complex regulatory network, offering new insights into how these molecules contribute to bacterial adaptation and pathogenesis.

  PublisherOA PDFDOI

• Transcriptional and post-transcriptional mechanisms modulate cyclopropane fatty acid synthase through small RNAs in <i>Escherichia coli</i>

  Journal of Bacteriology · 2024-07-09 · 4 citations

  articleOpen accessSenior author

  ABSTRACT The small RNA (sRNA) RydC strongly activates cfa , which encodes the cyclopropane fatty acid synthase. Previous work demonstrated that RydC activation of cfa increases the conversion of unsaturated fatty acids to cyclopropanated fatty acids in membrane lipids and changes the biophysical properties of membranes, making cells more resistant to acid stress. The regulators that control RydC synthesis had not previously been identified. In this study, we identify a GntR-family transcription factor, YieP, that represses rydC transcription. YieP positively autoregulates its own transcription and indirectly regulates cfa through RydC. We further identify additional sRNA regulatory inputs that contribute to the control of RydC and cfa . The translation of yieP is repressed by the Fnr-dependent sRNA, FnrS, making FnrS an indirect activator of rydC and cfa . Conversely, RydC activity on cfa is antagonized by the OmpR-dependent sRNA OmrB. Altogether, this work illuminates a complex regulatory network involving transcriptional and post-transcriptional inputs that link the control of membrane biophysical properties to multiple environmental signals. IMPORTANCE Bacteria experience many environmental stresses that challenge their membrane integrity. To withstand these challenges, bacteria sense what stress is occurring and mount a response that protects membranes. Previous work documented the important roles of small RNA (sRNA) regulators in membrane stress responses. One sRNA, RydC, helps cells cope with membrane-disrupting stresses by promoting changes in the types of lipids incorporated into membranes. In this study, we identified a regulator, YieP, that controls when RydC is produced and additional sRNA regulators that modulate YieP levels and RydC activity. These findings illuminate a complex regulatory network that helps bacteria sense and respond to membrane stress.

  PublisherDOI

• Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-10-22 · 1 citations

  preprintOpen access

  Many bacterial traits important to host-microbe symbiosis are determined by genes carried on extrachromosomal replicons such as plasmids, chromids, and integrative and conjugative elements. Multiple such replicons often coexist within a single cell and, due to horizontal mobility, have patterns of variation and evolutionary histories that are distinct from each other and from the bacterial chromosome. In nitrogen-fixing Rhizobium, genes carried on multiple plasmids make up almost 50% of the genome, are necessary for the formation of symbiosis, and underlie bacterial traits including host plant benefits. Thus the genomics and transmission of plasmids in Rhizobium underlie the ecology and evolution of this important model symbiont. Here we leverage a natural population of clover-associated Rhizobium in which partner quality has declined in response to long-term nitrogen fertilization. We use 62 novel, reference-quality genomes to characterize 257 replicons in the plasmidome and study their genomics and transmission patterns. We find that, of the four most frequent plasmid types, two (types II &amp; III) have more stable size, larger core genomes, and track the chromosomal phylogeny (display more vertical transmission), while others (types I &amp; IV – the symbiosis plasmid, or pSym) vary substantially in size, shared gene content, and have phylogenies consistent with frequent horizontal transmission. We also find differentiation in pSym subtypes driven by long-term nitrogen fertilization. Our results highlight the variation in plasmid transmission dynamics within a single symbiont and implicate plasmid horizontal transmission in the evolution of partner quality.

  PublisherOA PDFDOI

• Small RNAs positively and negatively control transcription elongation through modulation of Rho utilization site accessibility

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-02-03 · 4 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Bacteria use a multi-layered regulatory strategy to precisely and rapidly tune gene expression in response to environmental cues. Small RNAs (sRNAs) form an important layer of gene expression control and most act post-transcriptionally to control translation and stability of mRNAs. We have shown that at least five different sRNAs in Escherichia coli regulate the cyclopropane fatty acid synthase ( cfa ) mRNA. These sRNAs bind at different sites in the long 5’ untranslated region (UTR) of cfa mRNA and previous work suggested that they modulate RNase E-dependent mRNA turnover. Recently, the cfa 5’ UTR was identified as a site of Rho-dependent transcription termination, leading us to hypothesize that the sRNAs might also regulate cfa transcription elongation. In this study we find that a pyrimidine-rich region flanked by sRNA binding sites in the cfa 5’ UTR is required for premature Rho-dependent termination. We discovered that both the activating sRNA RydC and repressing sRNA CpxQ regulate cfa primarily by modulating Rho-dependent termination of cfa transcription, with only a minor effect on RNase E-mediated turnover of cfa mRNA. A stem-loop structure in the cfa 5’ UTR sequesters the pyrimidine-rich region required for Rho-dependent termination. CpxQ binding to the 5’ portion of the stem increases Rho-dependent termination whereas RydC binding downstream of the stem decreases termination. These results reveal the versatile mechanisms sRNAs use to regulate target gene expression at transcriptional and post-transcriptional levels and demonstrate that regulation by sRNAs in long UTRs can involve modulation of transcription elongation. Importance Bacteria respond to stress by rapidly regulating gene expression. Regulation can occur through control of messenger RNA (mRNA) production (transcription elongation), stability of mRNAs, or translation of mRNAs. Bacteria can use small RNAs (sRNAs) to regulate gene expression at each of these steps, but we often do not understand how this works at a molecular level. In this study, we find that sRNAs in Escherichia coli regulate gene expression at the level of transcription elongation by promoting or inhibiting transcription termination by a protein called Rho. These results help us understand new molecular mechanisms of gene expression regulation in bacteria.

  PublisherOA PDFDOI

Recent grants

• Molecular Determinants of Regulatory Hierarchy for Bacterial Small RNAs

  NIH · $2.4M · 2010–2022

• NIH Grant R01GM120182

  NIH · $1.2M · 2021

• Quantitative Imaging and Modeling of Regulation by Bacterial Small RNA

  NIH · $1.1M · 2015–2019

• Small RNA Regulation in Bacteria

  NIH · $2.6M · 2021–2031

Frequent coauthors

• Taekjip Ha

  Howard Hughes Medical Institute

  19 shared

• Muhammad S. Azam

  University of Missouri

  18 shared

• Susan Gottesman

  Center for Cancer Research

  14 shared

• Anustup Poddar

  Johns Hopkins Medicine

  13 shared

• Maksym Bobrovskyy

  University of Chicago

  13 shared

• Divya Balasubramanian

  Periyar Maniammai Institute of Science & Technology

  11 shared

• Xiangqian Ma

  University of Illinois Urbana-Champaign

  10 shared

• Jingyi Fei

  University of Chicago

  10 shared

Labs

• Vanderpool LabPI

Awards & honors

• 2018 Charles G Miller Professorial Scholar
• 2013 Helen Corley Petit Scholar, College of Liberal Arts and…