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Raul Salinas

Research Associate, Senior
Biochemistry
307 Research Drive, Nanaline H. Duke Building, Room 243, Durham, NC 27710

Selected Publications


Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp.

Journal Article Nucleic Acids Res · July 8, 2024 Nucleoid-associated proteins (NAPs) play central roles in bacterial chromosome organization and DNA processes. The Escherichia coli YejK protein is a highly abundant, yet poorly understood NAP. YejK proteins are conserved among Gram-negative bacteria but s ... Full text Link to item Cite

Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site.

Journal Article Nucleic Acids Res · February 9, 2024 Transcription regulators play central roles in orchestrating responses to changing environmental conditions. Recently the Caulobacter crescentus transcription activator DriD, which belongs to the newly defined WYL-domain family, was shown to regulate DNA d ... Full text Link to item Cite

M. mazei glutamine synthetase and glutamine synthetase-GlnK1 structures reveal enzyme regulation by oligomer modulation.

Journal Article Nat Commun · November 15, 2023 Glutamine synthetases (GS) play central roles in cellular nitrogen assimilation. Although GS active-site formation requires the oligomerization of just two GS subunits, all GS form large, multi-oligomeric machines. Here we describe a structural dissection ... Full text Link to item Cite

Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding.

Journal Article Nat Commun · November 9, 2023 The mycobacterial repressor, DarR, a TetR family regulator (TFR), was the first transcription regulator shown to bind c-di-AMP. However, the molecular basis for this interaction and the mechanism involved in DNA binding by DarR remain unknown. Here we desc ... Full text Link to item Cite

Structure of the T. brucei kinetoplastid RNA editing substrate-binding complex core component, RESC5.

Journal Article PLoS One · 2023 Kinetoplastid protists such as Trypanosoma brucei undergo an unusual process of mitochondrial uridine (U) insertion and deletion editing termed kinetoplastid RNA editing (kRNA editing). This extensive form of editing, which is mediated by guide RNAs (gRNAs ... Full text Link to item Cite

Molecular Analysis of pSK1 par: A Novel Plasmid Partitioning System Encoded by Staphylococcal Multiresistance Plasmids.

Journal Article J Mol Biol · October 15, 2022 The segregation of prokaryotic plasmids typically requires a centromere-like site and two proteins, a centromere-binding protein (CBP) and an NTPase. By contrast, a single 245 residue Par protein mediates partition of the prototypical staphylococcal multir ... Full text Link to item Cite

Allosteric regulation of glycogen breakdown by the second messenger cyclic di-GMP.

Journal Article Nat Commun · October 3, 2022 Streptomyces are our principal source of antibiotics, which they generate concomitant with a complex developmental transition from vegetative hyphae to spores. c-di-GMP acts as a linchpin in this transition by binding and regulating the key developmental r ... Full text Link to item Cite

Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria.

Journal Article Nat Commun · July 1, 2022 Featured Publication How bacteria sense and respond to nitrogen levels are central questions in microbial physiology. In Gram-positive bacteria, nitrogen homeostasis is controlled by an operon encoding glutamine synthetase (GS), a dodecameric machine that assimilates ammonium ... Full text Link to item Cite

ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD.

Journal Article Genes Dev · May 1, 2022 DNA damage repair systems are critical for genomic integrity. However, they must be coordinated with DNA replication and cell division to ensure accurate genomic transmission. In most bacteria, this coordination is mediated by the SOS response through LexA ... Full text Link to item Cite

DNA mismatches reveal conformational penalties in protein-DNA recognition.

Journal Article Nature · November 2020 Featured Publication Transcription factors recognize specific genomic sequences to regulate complex gene-expression programs. Although it is well-established that transcription factors bind to specific DNA sequences using a combination of base readout and shape recognition, so ... Full text Open Access Link to item Cite

The Gut of Healthy Infants in the Community as a Reservoir of ESBL and Carbapenemase-Producing Bacteria.

Journal Article Antibiotics (Basel, Switzerland) · May 2020 The recent rapid rise of multi-drug resistant Enterobacteriaceae (MDR-E) is threatening the treatment of common infectious diseases. Infections with such strains lead to increased mortality and morbidity. Using a cross-sectional study, we aimed to estimate ... Full text Open Access Cite

Infrared Spectroscopic Observation of a G-C+ Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions.

Journal Article Angew Chem Int Ed Engl · August 26, 2019 Hoogsteen DNA base pairs (bps) are an alternative base pairing to canonical Watson-Crick bps and are thought to play important biochemical roles. Hoogsteen bps have been reported in a handful of X-ray structures of protein-DNA complexes. However, there are ... Full text Open Access Link to item Cite

An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease.

Journal Article Cell Host Microbe · August 8, 2018 Pathogens have been a strong driving force for natural selection. Therefore, understanding how human genetic differences impact infection-related cellular traits can mechanistically link genetic variation to disease susceptibility. Here we report the Hi-HO ... Full text Open Access Link to item Cite

Human genetic and metabolite variation reveals that methylthioadenosine is a prognostic biomarker and an inflammatory regulator in sepsis.

Journal Article Sci Adv · March 2017 Sepsis is a deleterious inflammatory response to infection with high mortality. Reliable sepsis biomarkers could improve diagnosis, prognosis, and treatment. Integration of human genetics, patient metabolite and cytokine measurements, and testing in a mous ... Full text Open Access Link to item Cite

A cellular genome-wide association study reveals human variation in microtubule stability and a role in inflammatory cell death.

Journal Article Mol Biol Cell · January 2014 Pyroptosis is proinflammatory cell death that occurs in response to certain microbes. Activation of the protease caspase-1 by molecular platforms called inflammasomes is required for pyroptosis. We performed a cellular genome-wide association study (GWAS) ... Full text Open Access Link to item Cite

Epstein-Barr virus induces global changes in cellular mRNA isoform usage that are important for the maintenance of latency.

Journal Article J Virol · November 2013 Oncogenic viruses promote cell proliferation through the dramatic reorganization of host transcriptomes. In addition to regulating mRNA abundance, changes in mRNA isoform usage can have a profound impact on the protein output of the transcriptome. Using Ep ... Full text Open Access Link to item Cite

Analysis of Epstein-Barr virus-regulated host gene expression changes through primary B-cell outgrowth reveals delayed kinetics of latent membrane protein 1-mediated NF-κB activation.

Journal Article J Virol · October 2012 Epstein-Barr virus (EBV) is an oncogenic human herpesvirus that dramatically reorganizes host gene expression to immortalize primary B cells. In this study, we analyzed EBV-regulated host gene expression changes following primary B-cell infection, both dur ... Full text Open Access Link to item Cite

SplicerEX: a tool for the automated detection and classification of mRNA changes from conventional and splice-sensitive microarray expression data.

Journal Article RNA · August 2012 The key postulate that one gene encodes one protein has been overhauled with the discovery that one gene can generate multiple RNA transcripts through alternative mRNA processing. In this study, we describe SplicerEX, a novel and uniquely motivated algorit ... Full text Open Access Link to item Cite

The Epstein-Barr virus (EBV)-induced tumor suppressor microRNA MiR-34a is growth promoting in EBV-infected B cells.

Journal Article J Virol · June 2012 Epstein-Barr virus (EBV) infection of primary human B cells drives their indefinite proliferation into lymphoblastoid cell lines (LCLs). B cell immortalization depends on expression of viral latency genes, as well as the regulation of host genes. Given the ... Full text Open Access Link to item Cite

Role of inositol 1,4,5-triphosphate signalling in gravitropic and phototropic gene expression.

Journal Article Plant, cell & environment · December 2010 Plants sense light and gravity to orient their direction of growth. One common component in the early events of both phototropic and gravitropic signal transduction is activation of phospholipase C (PLC), which leads to an increase in inositol 1,4,5-tripho ... Full text Open Access Cite

Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp.

Journal Article Nucleic Acids Res · July 8, 2024 Nucleoid-associated proteins (NAPs) play central roles in bacterial chromosome organization and DNA processes. The Escherichia coli YejK protein is a highly abundant, yet poorly understood NAP. YejK proteins are conserved among Gram-negative bacteria but s ... Full text Link to item Cite

Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site.

Journal Article Nucleic Acids Res · February 9, 2024 Transcription regulators play central roles in orchestrating responses to changing environmental conditions. Recently the Caulobacter crescentus transcription activator DriD, which belongs to the newly defined WYL-domain family, was shown to regulate DNA d ... Full text Link to item Cite

M. mazei glutamine synthetase and glutamine synthetase-GlnK1 structures reveal enzyme regulation by oligomer modulation.

Journal Article Nat Commun · November 15, 2023 Glutamine synthetases (GS) play central roles in cellular nitrogen assimilation. Although GS active-site formation requires the oligomerization of just two GS subunits, all GS form large, multi-oligomeric machines. Here we describe a structural dissection ... Full text Link to item Cite

Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding.

Journal Article Nat Commun · November 9, 2023 The mycobacterial repressor, DarR, a TetR family regulator (TFR), was the first transcription regulator shown to bind c-di-AMP. However, the molecular basis for this interaction and the mechanism involved in DNA binding by DarR remain unknown. Here we desc ... Full text Link to item Cite

Structure of the T. brucei kinetoplastid RNA editing substrate-binding complex core component, RESC5.

Journal Article PLoS One · 2023 Kinetoplastid protists such as Trypanosoma brucei undergo an unusual process of mitochondrial uridine (U) insertion and deletion editing termed kinetoplastid RNA editing (kRNA editing). This extensive form of editing, which is mediated by guide RNAs (gRNAs ... Full text Link to item Cite

Molecular Analysis of pSK1 par: A Novel Plasmid Partitioning System Encoded by Staphylococcal Multiresistance Plasmids.

Journal Article J Mol Biol · October 15, 2022 The segregation of prokaryotic plasmids typically requires a centromere-like site and two proteins, a centromere-binding protein (CBP) and an NTPase. By contrast, a single 245 residue Par protein mediates partition of the prototypical staphylococcal multir ... Full text Link to item Cite

Allosteric regulation of glycogen breakdown by the second messenger cyclic di-GMP.

Journal Article Nat Commun · October 3, 2022 Streptomyces are our principal source of antibiotics, which they generate concomitant with a complex developmental transition from vegetative hyphae to spores. c-di-GMP acts as a linchpin in this transition by binding and regulating the key developmental r ... Full text Link to item Cite

Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria.

Journal Article Nat Commun · July 1, 2022 Featured Publication How bacteria sense and respond to nitrogen levels are central questions in microbial physiology. In Gram-positive bacteria, nitrogen homeostasis is controlled by an operon encoding glutamine synthetase (GS), a dodecameric machine that assimilates ammonium ... Full text Link to item Cite

ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD.

Journal Article Genes Dev · May 1, 2022 DNA damage repair systems are critical for genomic integrity. However, they must be coordinated with DNA replication and cell division to ensure accurate genomic transmission. In most bacteria, this coordination is mediated by the SOS response through LexA ... Full text Link to item Cite

DNA mismatches reveal conformational penalties in protein-DNA recognition.

Journal Article Nature · November 2020 Featured Publication Transcription factors recognize specific genomic sequences to regulate complex gene-expression programs. Although it is well-established that transcription factors bind to specific DNA sequences using a combination of base readout and shape recognition, so ... Full text Open Access Link to item Cite

The Gut of Healthy Infants in the Community as a Reservoir of ESBL and Carbapenemase-Producing Bacteria.

Journal Article Antibiotics (Basel, Switzerland) · May 2020 The recent rapid rise of multi-drug resistant Enterobacteriaceae (MDR-E) is threatening the treatment of common infectious diseases. Infections with such strains lead to increased mortality and morbidity. Using a cross-sectional study, we aimed to estimate ... Full text Open Access Cite

Infrared Spectroscopic Observation of a G-C+ Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions.

Journal Article Angew Chem Int Ed Engl · August 26, 2019 Hoogsteen DNA base pairs (bps) are an alternative base pairing to canonical Watson-Crick bps and are thought to play important biochemical roles. Hoogsteen bps have been reported in a handful of X-ray structures of protein-DNA complexes. However, there are ... Full text Open Access Link to item Cite

An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease.

Journal Article Cell Host Microbe · August 8, 2018 Pathogens have been a strong driving force for natural selection. Therefore, understanding how human genetic differences impact infection-related cellular traits can mechanistically link genetic variation to disease susceptibility. Here we report the Hi-HO ... Full text Open Access Link to item Cite

Human genetic and metabolite variation reveals that methylthioadenosine is a prognostic biomarker and an inflammatory regulator in sepsis.

Journal Article Sci Adv · March 2017 Sepsis is a deleterious inflammatory response to infection with high mortality. Reliable sepsis biomarkers could improve diagnosis, prognosis, and treatment. Integration of human genetics, patient metabolite and cytokine measurements, and testing in a mous ... Full text Open Access Link to item Cite

A cellular genome-wide association study reveals human variation in microtubule stability and a role in inflammatory cell death.

Journal Article Mol Biol Cell · January 2014 Pyroptosis is proinflammatory cell death that occurs in response to certain microbes. Activation of the protease caspase-1 by molecular platforms called inflammasomes is required for pyroptosis. We performed a cellular genome-wide association study (GWAS) ... Full text Open Access Link to item Cite

Epstein-Barr virus induces global changes in cellular mRNA isoform usage that are important for the maintenance of latency.

Journal Article J Virol · November 2013 Oncogenic viruses promote cell proliferation through the dramatic reorganization of host transcriptomes. In addition to regulating mRNA abundance, changes in mRNA isoform usage can have a profound impact on the protein output of the transcriptome. Using Ep ... Full text Open Access Link to item Cite

Analysis of Epstein-Barr virus-regulated host gene expression changes through primary B-cell outgrowth reveals delayed kinetics of latent membrane protein 1-mediated NF-κB activation.

Journal Article J Virol · October 2012 Epstein-Barr virus (EBV) is an oncogenic human herpesvirus that dramatically reorganizes host gene expression to immortalize primary B cells. In this study, we analyzed EBV-regulated host gene expression changes following primary B-cell infection, both dur ... Full text Open Access Link to item Cite

SplicerEX: a tool for the automated detection and classification of mRNA changes from conventional and splice-sensitive microarray expression data.

Journal Article RNA · August 2012 The key postulate that one gene encodes one protein has been overhauled with the discovery that one gene can generate multiple RNA transcripts through alternative mRNA processing. In this study, we describe SplicerEX, a novel and uniquely motivated algorit ... Full text Open Access Link to item Cite

The Epstein-Barr virus (EBV)-induced tumor suppressor microRNA MiR-34a is growth promoting in EBV-infected B cells.

Journal Article J Virol · June 2012 Epstein-Barr virus (EBV) infection of primary human B cells drives their indefinite proliferation into lymphoblastoid cell lines (LCLs). B cell immortalization depends on expression of viral latency genes, as well as the regulation of host genes. Given the ... Full text Open Access Link to item Cite

Role of inositol 1,4,5-triphosphate signalling in gravitropic and phototropic gene expression.

Journal Article Plant, cell & environment · December 2010 Plants sense light and gravity to orient their direction of growth. One common component in the early events of both phototropic and gravitropic signal transduction is activation of phospholipase C (PLC), which leads to an increase in inositol 1,4,5-tripho ... Full text Open Access Cite

FoxJ1-dependent gene expression is required for differentiation of radial glia into ependymal cells and a subset of astrocytes in the postnatal brain.

Journal Article Development (Cambridge, England) · December 2009 Neuronal specification occurs at the periventricular surface of the embryonic central nervous system. During early postnatal periods, radial glial cells in various ventricular zones of the brain differentiate into ependymal cells and astrocytes. However, m ... Full text Cite

Analysis of neuronal proliferation, migration and differentiation in the postnatal brain using equine infectious anemia virus-based lentiviral vectors.

Journal Article Gene therapy · August 2009 Ongoing neurogenesis in discrete sectors of the adult central nervous system depends on the mitotic activity of an elusive population of adult stem cells. The existence of adult neural stem cells provides an alternative approach to transplantation of embry ... Full text Cite

The fast and transient transcriptional network of gravity and mechanical stimulation in the Arabidopsis root apex.

Journal Article Plant physiology · September 2004 Plant root growth is affected by both gravity and mechanical stimulation (Massa GD, Gilroy S [2003] Plant J 33: 435-445). A coordinated response to both stimuli requires specific and common elements. To delineate the transcriptional response mechanisms, we ... Full text Open Access Cite

Regulation of transcription in roots of Arabidopsis gravity mutant

Journal Article ASGSB bulletin : publication of the American Society for Gravitational and Space Biology Cite