Justin A. North's research while affiliated with The Ohio State University and other places

Publications (57)

Article
Bacterial production of gaseous hydrocarbons such as ethylene and methane affects soil environments and atmospheric climate. We demonstrate that biogenic methane and ethylene from terrestrial and freshwater bacteria are directly produced by a previously unknown methionine biosynthesis pathway. This pathway, present in numerous species, uses a nitro...
Article
Full-text available
S-adenosyl-L-methionine (SAM) is a necessary co-substrate for numerous essential enzymatic reactions including protein and nucleotide methylations, secondary metabolite synthesis, and radical-mediated processes. Radical SAM enzymes produce 5'-deoxyadenosine, and SAM-dependent enzymes for polyamine, neurotransmitter, and quorum sensing compound synt...
Article
The enzyme ribulose 1,5‐bisphosphate carboxylase/oxygenase (RuBisCO) and its central role in capturing atmospheric CO2 via the Calvin-Benson-Bassham (CBB) cycle has been well-studied. Previously, a form II RuBisCO from Rhodopseudomonas palustris, a facultative anaerobic bacterium, was shown to assemble into a hexameric holoenzyme. Unlike previous s...
Article
Full-text available
5′-Methyl-thioadenosine (MTA) is a dead-end, sulfur-containing metabolite and cellular inhibitor that arises from S-adenosyl-l-methionine-dependent reactions. Recent studies have indicated that there are diverse bacterial methionine salvage pathways (MSPs) for MTA detoxification and sulfur salvage. Here, via a combination of gene deletions and dire...
Article
Numerous cellular processes involving S-adenosyl-l-methionine result in the formation of the toxic by-product, 5'-methylthioadenosine (MTA). To prevent inhibitory MTA accumulation and retain biologically available sulfur, most organisms possess the "universal" methionine salvage pathway (MSP). However, the universal MSP is inherently aerobic due to...
Chapter
Nucleosomes are the fundamental organizing unit of all eukaryotic genomes. Understanding how proteins gain access to DNA-binding sites located within nucleosomes is important for understanding DNA processing including transcription, replication, and repair. Single-molecule total internal reflection fluorescence (smTIRF) microscopy measurements can...
Article
Full-text available
Unlabelled: Rhodospirillum rubrum possesses a novel oxygen-independent, aerobic methionine salvage pathway (MSP) for recycling methionine from 5-methylthioadenosine (MTA), the MTA-isoprenoid shunt. This organism can also metabolize MTA as a sulfur source under anaerobic conditions, suggesting that the MTA-isoprenoid shunt may also function anaerob...
Data
Potential anaerobic MTA metabolism in other organisms. BLASTp alignment of R. rubrum MTXu-5P sulfurylase (1, Rru_A2000, cupin) and MTRu-1P isomerase (2, Rru_A1998, RLP) visualized using Seed Viewer 2.0. Download
Data
Supplemental materials and methods detailing proteomics procedures as well as strain construction. Download
Data
Identification of purine salvage nucleosides and bases. (A) HPLC analysis at 260-nm detection of known standards. (B) HPLC analysis of purines produced by R. rubrum wild-type strain after 120 min post-anaerobic feeding with MTA before treatment with xanthine oxidase (− Xan Ox) and after treatment with xanthine oxidase (+ Xan Ox). The hypoxanthine p...
Data
Proteins observed to change in abundance level in response to MTA. NSAF is the normalized spectral abundance factor. Av. Adj. NSAF is the average of the NSAFs from the 4 technical replicates for MTA- and sulfate-fed cells.
Data
All proteins observed by deep proteomics. NSAF is the normalized spectral abundance factor. Av. Adj. NSAF is the average of the NSAFs from the 4 technical replicates for MTA- and sulfate-fed cells. PI, isoelectric point; MW, molecular weight; COG, clusters of orthologous groups.
Data
Cellular chemotaxis and motility proteins regulated by MTA. Green, protein increased in abundance; black, protein observed but no change in abundance; gray, protein not observed by deep proteomics. Numerous proteins of the rotor complex of the flagellar motor were affected by MTA, including the C-ring (FliG, Rru_A0544, 2-fold; FliN, Rru_A0542, 1.5-...
Data
Statistical analysis of proteins identified by deep proteomics. (A) Venn diagram of proteins observed only in sulfate-grown cells, only in MTA-grown cells, and in both. (B) Distribution of identified proteins based on their cellular localization. The cellular localization pattern of expressed proteins in MTA- and sulfate-grown cells was investigate...
Data
Metabolite identification by radiochromatography. (A) Reversed-phase separation and 14C radiometric detection of MTA metabolism standards. Bottom trace, [methyl-14C]MTA treated with MTA phosphorylase (Rru_A0361) to produce MTR-1P (peak 1). Middle trace, MTR-1P treated with MTR-1P isomerase (Rru_A0360) to produce MTRu-1P (peak 2). Top trace, MTRu-1P...
Data
STRING analysis of MetINQ homologues. (A) Protein-protein interactions of putative methionine transport proteins in R. rubrum were analyzed by STRING v10 analysis using the following proteins as the query: Rru_A0778, lipoprotein YaeC; Rru_A0779, extracellular solute-binding protein; Rru_A0780, binding-protein-dependent transport system inner membra...
Article
A key limitation of electron paramagnetic resonance (EPR), an established and powerful tool for studying atomic-scale biomolecular structure and dynamics is its poor sensitivity, samples containing in excess of 10^12 labeled biomolecules are required in typical experiments. In contrast, single molecule measurements provide improved insights into he...
Article
Ribulose 1, 5-bisphosphate carboxylase/oxygenase (RubisCO) is a critical yet severely inefficient enzyme that catalyzes the fixation of virtually all of the carbon found on Earth. Here, we report a functional metagenomic selection that recovers physiologically-active RubisCO molecules directly from uncultivated and largely unknown members of natura...
Article
Full-text available
All organisms possess fundamental metabolic pathways to ensure that needed carbon and sulfur compounds are provided to the cell in the proper chemical form and oxidation state. For most organisms capable of using CO2 as sole source of carbon, ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) catalyzes primary carbon dioxide assimilat...
Article
Signaling associated with transcription activation occurs through posttranslational modification of histones and is best exemplified by lysine acetylation. Lysines are acetylated in histone tails and the core domain/lateral surface of histone octamers. While acetylated lysines in histone tails are frequently recognized by other factors referred to...
Article
Full-text available
Nucleosome unwrapping dynamics provide transient access to the complexes involved in DNA transcription, repair and replication, while regulation of nucleosome unwrapping modulates occupancy of these complexes. Histone H3 is phosphorylated at Tyrosine 41 (H3Y41ph) and Threonine 45 (H3T45ph). H3Y41ph is implicated in regulating transcription, while H...
Article
Histone post translational modifications (PTMs) regulate DNA transcription, replication and repair. A number of histone PTMs have been identified within the DNA entry-exit region of the nucleosome including phosphorylation of H3 at tyrosine 41 (H3Y41ph) and threonine 45 (H3T45ph). Each of these modifications are implicated to occur with H3K56ac, wh...
Article
Electron paramagnetic resonance (EPR) is an established and powerful tool for studying atomic-scale biomolecular structure and dynamics. Yet it requires a homogenous sample size of ∼10∧15 spin labeled biomolecules. Single molecule measurements provide improved insights into heterogeneous behaviors that can be masked by ensemble measurements and are...
Article
Site specific DNA binding complexes must bind their DNA target sites and then reside there for a sufficient amount of time for proper regulation of DNA processing including transcription, replication and DNA repair. In eukaryotes, the occupancy of DNA binding complexes at their target sites is regulated by chromatin structure and dynamics. Methodol...
Article
Full-text available
Nucleosomes contain ∼146 bp of DNA wrapped around a histone protein octamer that controls DNA accessibility to transcription and repair complexes. Posttranslational modification (PTM) of histone proteins regulates nucleosome function. To date, only modest changes in nucleosome structure have been directly attributed to histone PTMs. Histone residue...
Article
Guidelines for submitting commentsPolicy: Comments that contribute to the discussion of the article will be posted within approximately three business days. We do not accept anonymous comments. Please include your email address; the address will not be displayed in the posted comment. Cell Press Editors will screen the comments to ensure that they...
Article
Full-text available
The Tudor domain of human PHF1 recognizes trimethylated lysine 36 of histone H3 (H3K36me3). This interaction modulates the methyltransferase activity of the PRC2 complex and has a role in retention of PHF1 at DNA damage sites. We have previously determined the structural basis for the association of Tudor with a methylated histone peptide. Here we...
Article
Full-text available
Transcription factors (TF) bind DNA-target sites within promoters to activate gene expression. TFs target their DNA-recognition sequences with high specificity by binding with resident times of up to hours in vitro. However, in vivo TFs can exchange on the order of seconds. The factors that regulate TF dynamics in vivo and increase dissociation rat...
Article
Chromatin is a supramolecular assembly of DNA and histone proteins, organized into nucleosome repeat units. The dynamics of chromatin organization regulates DNA accessibility to eukaryotic transcription and DNA repair complexes. However, the structural and dynamic properties of chromatin at high concentrations characteristic of the cellular environ...
Article
Full-text available
Double-strand breaks (DSB) occur in chromatin following replication fork collapse and chemical or physical damage [Symington and Gautier (Double-strand break end resection and repair pathway choice. Annu. Rev. Genet. 2011;45:247–271.)] and may be repaired by homologous recombination (HR) and non-homologous end-joining. Nucleosomes are the fundament...
Article
Full-text available
Lens epithelium-derived growth factor (LEDGF/p75) tethers lentiviral preintegration complexes (PICs) to chromatin and is essential for effective HIV-1 replication. LEDGF/p75 interactions with lentiviral integrases are well characterized, but the structural basis for how LEDGF/p75 engages chromatin is unknown. We demonstrate that cellular LEDGF/p75...
Article
Transcription factors (TFs) play a central role in regulating the transcriptional state of gene. However, TFs are sterically occluded from their target sequences when it is wrapped around the histone octamer into a nucleosome. The combination of nucleosomal DNA unwrapping fluctuations and the high DNA sequence specificity of TFs facilitate TF to bi...
Article
Full-text available
Eukaryotic genomes are repetitively wrapped into nucleosomes that then regulate access of transcription and DNA repair complexes to DNA. The mechanisms that regulate extrinsic protein interactions within nucleosomes are unresolved. We demonstrate that modulation of the nucleosome unwrapping rate regulates protein binding within nucleosomes. Histone...
Article
Somatic hypermutation (SHM) of immunoglobulin (Ig) genes is initiated by the activation-induced cytidine deaminase (AID). However, the influence of chromatin on SHM remains enigmatic. Our previous cell-free studies indicated that AID cannot access nucleosomal DNA in the absence of transcription. We have now investigated the influence of nucleosome...
Article
Genetic information in humans is encoded within DNA molecules that is wrapped around histone octamer proteins and compacted into a highly conserved structural polymer, chromatin. The physical and material properties of chromatin appear to influence gene expression by altering the accessibility of proteins to the DNA. The tails of the histones are f...
Article
Full-text available
A major challenge to achieving positional control of fluid borne submicron sized objects is regulating their Brownian fluctuations. We present a magnetic-field-based trap that regulates the thermal fluctuations of superparamagnetic beads in suspension. Local domain-wall fields originating from patterned magnetic wires, whose strength and profile ar...
Article
Full-text available
Nucleosomes are stable DNA-histone protein complexes that must be unwrapped and disassembled for genome expression, replication, and repair. Histone posttranslational modifications (PTMs) are major regulatory factors of these nucleosome structural changes, but the molecular mechanisms associated with PTM function remains poorly understood. Here we...
Article
Full-text available
The expression, replication and repair of eukaryotic genomes require the fundamental organizing unit of chromatin, the nucleosome, to be unwrapped and disassembled. We have developed a quantitative model of nucleosome dynamics which provides a fundamental understanding of these DNA processes. We calibrated this model using results from high precisi...
Article
Full-text available
Nucleosomes, the fundamental units of chromatin structure, are regulators and barriers to transcription, replication and repair. Post-translational modifications (PTMs) of the histone proteins within nucleosomes regulate these DNA processes. Histone H3(T118) is a site of phosphorylation [H3(T118ph)] and is implicated in regulation of transcription...
Article
Nitrogen vacancy centers in diamond are single-spin systems that are stable under ambient conditions with strong optical spin transitions, making them optimal for room-temperature detection of nanoscale magnetic fields using optically detected magnetic resonance (ODMR). We use these ensembles of diamond spins as a scanned probe magnetometer to map...
Article
Full-text available
Posttranslational modification (PTM) of histones plays a central role in genome regulation. Engineering histones with defined PTMs on one residue or on multiple residues is crucial for understanding their function within nucleosomes and chromatin. We introduce a sequential native chemical ligation strategy that is suitable for the preparation of fu...
Article
Full-text available
Histone post-translational modifications are essential for regulating and facilitating biological processes such as RNA transcription and DNA repair. Fifteen modifications are located in the DNA-histone dyad interface and include the acetylation of H3-K115 (H3-K115Ac) and H3-K122 (H3-K122Ac), but the functional consequences of these modifications a...
Article
Full-text available
The activation-induced cytidine deaminase (AID) initiates somatic hypermutation, class-switch recombination, and gene conversion of immunoglobulin genes. In vitro, AID has been shown to target single-stranded DNA, relaxed double-stranded DNA, when transcribed, or supercoiled DNA. To simulate the in vivo situation more closely, we have introduced tw...
Article
The nucleosome is the fundamental unit of DNA compaction in eukaryotes by which 147 base pairs of DNA wrap 1.7 times around a protein complex called the histone octamer. Numerous chemical modifications are found in vivo that alter octamer surface charge and shape. One such modification is phosphorylation of histone H3 residue Thr 118 located in the...
Article
It is known that the free surface of an axisymmetric viscous film flowing down the outside of a thin vertical fiber under the influence of gravity becomes unstable to interfacial perturbations. We present an experimental study using fluids with different densities, surface tensions, and viscosities to investigate the growth and dynamics of these in...
Article
We experimentally examine the motion of an annular jet of viscous fluid flowing down the outside of a thin, vertical fiber. As other authors have observed, perturbations develop along the free surface of the jet; our focus is on the instability that leads to the formation of these perturbations. We observe a striking transition in the perturbation...

Citations

... gestii strain DSM 11169 nif and anf loci were obtained from Genbank genome accession PRJNA599378. Protein phylogenetic analyses were performed on a subset of NifHDK homologs previously designated as belonging to nitrogenase-like protein groups I-IV [21,22]. Following ClustalW [23] analysis, the resulting alignments were assembled into maximum-likelihood trees using the LG + G substitution model [24] Microorganisms 2022, 10, 869 5 of 18 with 100 replicates. ...
... Examining the gene ontology (GO) terms of these 86 inter-species common genes (Table S8, Sheet 4), we highlight seven genes involved in metabolism of small molecules, including EHI_000720 which encodes a 5 -methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase. It is involved in the S-adenosyl-L-methionine (SAM, AdoMet) cycle, which recycles S-adenosyl-L-homocysteine back to SAM, and in salvage pathways for 5 -deoxyadenosine and S-methyl-5 -thioadenosine [58]. MTA/SAH nucleosidase plays a key role in the purine salvage pathway and in recycling of methylthio groups, the encoding gene (EHI_000720) is believed to have been acquired by the E. histolytica genome through lateral gene transfer (LGT) from a bacterial genome. ...
... In conclusion, the 5HAN S59F mutant analysis allowed key residues that reduced (Gly53−Glu57 residues, Val201−Phe202 residues) and increased (Phe59, Asp63−Phe64 residues) the flexibility by ≥0.1 nm to be identified (Table 1). Changes were found at loop 6 and in the loop between αB and βC, which is a critical region for gaseous substrate binding after RuBP enolization has been completed [18,63]. Moreover, the comparison between 4LF1 WT and 5HJX A47V allowed the identification of key residues that increased (Gly35, Lys330−Met331) and reduced (Val201−Phe202) RuBisCO form II fluctuation by more than 0.1 nm (Table 1), which can be attributed to A47V mutation and which has an effect on RuBisCO catalytic activity [63]. ...
... Apart from the canonical, universally oxygen-dependent MSP [see Sekowska et al. [2004]; Albers [2009]; Sekowska et al. [2018]], different alternative pathways have been described in the last years. For example, the aerobic/anaerobic "MTA-isoprenoid shunt" [Erb et al., 2012], the anaerobic "DHAP-ethylene shunt" [North et al., 2017], the aerobic "DHAP-methanethiol shunt" [Miller et al., 2018a], the "bifunctional DHAP shunt" [North et al., 2020] and a modified anaerobic MSP in methanogenic archaea [Miller et al., 2018b]. A nice overview of the different MSP pathways was recently provided by North et al. [2020] and Miller et al. [2018a]. ...
... One of the most interesting observations from our study was the increased levels of PGE1 and 59-methylthioadenosine under HG feeding. PGE1 is an endothelial permeability-increasing factor (37); 59-methylthioadenosine is a by-product of polyamine synthesis, and its accumulation can become toxic (38); and their enrichment might induce increased rumen epithelium permeability. Another interesting finding was the decreased concentrations of some beneficial compounds for the HG cows, such as a-tocotrienol, g-tocotrienol, and choline. ...
... The histone octamer and histone tetramer in this structure do not deviate significantly from the histone structure within the nucleosome (13). The combination of these studies indicate that hexasomes are unwrapped on one side by [30][31][32][33][34][35][36][37][38][39][40] bases and that the structure of the remaining histone core is not significantly altered by the removal of an H2A-H2B dimer. ...
... 5dAdo uptake in bacteria, to the best of our knowledge, has not been further characterized. In R. rubrum, it is assumed that MTA is taken up via Rapp the methionine transport complex (MetINQ) because proteins of this complex are enriched when cells grow on MTA as a sole sulphur source [North et al., 2016]. Furthermore, the MetINQ methionine transport complex is known for its substrate promiscuity [North et al., 2016]. ...
... Additionally, a second ecologically motivated functionbased screen was developed that also targets RubisCO activity (Varaljay et al., 2016). Since Varaljay et al. (2016) used a different host-vector system, this heterologous complementation based functional metagenomic screen likely expands the spectrum of detectable active RubisCOs (Varaljay et al., 2016). ...
... Since its discovery in 1945 [1], electron paramagnetic resonance (EPR) or electron spin resonance (ESR) has been extensively used to characterize molecular systems [2], quantum dots [3], metal complexes [4], organic radicals [5] or defects in solid-state systems [6]. Commonly, ESR consists of applying a constant frequency microwave field while a magnetic field is swept across spin-flip resonance transitions. ...
... rubrum has only form II Rubisco, which consists of two subunits encoded by the cbbM gene [66,69]. Surprisingly, this protein was able to function not only as Rubisco, but also as an enolase in the methionine utilization pathway (a methionine salvage pathway, MSP) anaerobic conditions [70,71]. ...