Biology subjects

Coates, J.

Publications and source records attributed to Coates, J..

12 recordsLinked to original sources

bioRxiv2026

Redirecting carbon and electron flow in methanogenic laboratory scale anaerobic digestors with hypophosphite

In anaerobic digestion, formate is a central electron carrier linking primary and secondary fermentation to methanogenesis. Efforts to alter methane production have largely focused on directly targeting methanogens, while disruption of other trophic levels is underexplored. We recently demonstrated that hypophosphite is a naturally occurring inhibitor of formate exchange in syntrophic methanogenic systems. Here, we investigated whether intercepting formate exchange using hypophosphite can modulate methane production in a complex fermentative methanogenic system and what the longer-term consequences are for the structure and function of the microbiome. Using continuous up-flow anaerobic sludge blanket (UASB) columns fed with whey, we found that 100 M hypophosphite resulted in a transient (17 days) reduction in methane production by 20% to 50%, while carbon and electron flow was redirected towards hydrogen and volatile fatty acids. Accumulation of propionate, butyrate, branched-chain fatty acids, and not acetate indicated disruption of syntrophic formate metabolism. Following recovery of methane production in hypophosphite treated columns, we increased hypophosphite concentrations to millimolar levels and saw no repeated suppression of methane production. 16S rDNA amplicon sequencing revealed that hypophosphite treatment did not cause significant changes to microbiome composition. Methanogenic activity assays revealed a loss of formatotrophic methanogenic capacity in hypophosphite treated columns. Together, these results show that specific inhibition of formate exchange between syntrophs and methanogens decouples fermentative and methanogenic processes without altering microbiome composition with carbon and electron flow to methane ultimately redirected through hydrogen or acetate. This work demonstrates that hypophosphite can intercept syntrophic formate exchange in an engineered system and that long- term treatment with hypophosphite redirects electron flow towards electron carriers other than formate.

microbiology↗

bioRxiv2026

Analysis of MIKC c -type MADS-box genes and proteins in the fern Ceratopteris richardii

The MIKCc subfamily of MADS-box proteins play a key role in flowering plant reproduction, specifying and patterning the floral organs. MIKCC genes have been identified in non-flowering plants, the number increasing with the amount of whole-genome sequencing information available, but MIKCc functions outside flowering plants are less well understood. In this study, we have cloned and sequenced 14 of the 21 MIKCc genes in the model fern Ceratopteris richardii and identified expressed cDNAs/transcripts for a further 6 genes, extending and correcting previous genome-and transcriptome analysis. We have identified that the majority of Ceratopteris MIKCc genes are expressed in the reproductive sporophyte, with some genes showing reproductive specificity. Using protein alignments and structural modelling, we have shown that Ceratopteris MIKCC proteins are structurally diverse, with over half the proteins possessing extended regions N-terminal to the MADS DNA binding domain, suggesting divergent functions or regulation.

Plant Biology↗

bioRxiv2025

Distinct Colitis-Associated Macrophages Drive NOD2-DependentBacterial Sensing and Gut Homeostasis

Single-cell studies have revealed that intestinal macrophages maintain gut homeostasis through the balanced actions of reactive (inflammatory) and tolerant (non-inflammatory) subpopulations. How such balance is impaired in inflammatory bowel diseases (IBD), including Crohns disease (CD) and ulcerative colitis (UC), remains unresolved. Here, we define colon-specific macrophage states and reveal the critical role of non-inflammatory colon-associated macrophages (niColAMs) in IBD recovery. Through trans-scale analyses--integrating computational transcriptomics, proteomics, and in vivo interventional studies--we identified GIV (CCDC88A) as a key regulator of niColAMs. GIV emerged as the top-ranked gene in niColAMs that physically and functionally interacts with NOD2, an innate immune sensor implicated in CD and UC. Myeloid-specific GIV depletion exacerbates infectious colitis, prolongs disease, and abolishes the protective effects of the NOD2 ligand, muramyl dipeptide, in colitis and sepsis models. Mechanistically, GIVs C-terminus binds the terminal leucine-rich repeat (LRR#10) of NOD2 and is required for NOD2 to dampen inflammation and clear microbes. The CD-associated 1007fs NOD2-variant, which lacks LRR#10, cannot bind GIV--providing critical insights into how this clinically relevant variant impairs microbial sensing and clearance. These findings illuminate a critical GIV-NOD2 axis essential for gut homeostasis and highlight its disruption as a driver of dysbiosis and inflammation in IBD.

immunology↗

bioRxiv2022

A description of the genus Denitromonas nom. rev.: Denitromonas iodatirespirans sp. nov. a novel iodate-reducing bacterium and two novel perchlorate-reducing bacteria Denitromonas halophila and Denitromonas ohlonensis isolated from San Francisco Bay intertidal mudflats.

The genus Denitromonas is currently a non-validated taxon that has been identified in several recent publications as members of microbial communities arising from marine environments. Very little is known about the biology of Denitromonas spp., and no pure cultures are presently found in any culture collections. The current epitaph of Denitromonas was given to the organism under the assumption that all members of this genus are denitrifying bacteria. This study performs phenotypic and genomic analyses on three new Denitromonas spp. isolated from tidal mudflats in the San Francisco Bay. We demonstrate that Denitromonas spp. are indeed all facultative denitrifying bacteria that utilize a variety of carbon sources such as acetate, lactate, and succinate. In addition, individual strains also use the esoteric electron acceptors perchlorate, chlorate, and iodate. Both 16S and Rps/Rpl phylogenetic analyses place Denitromonas spp. as a deep branching clade in the family Zoogloeaceae, separate from either Thauera spp., Azoarcus spp., or Aromatoleum spp. Genome sequencing reveals a G+C content ranging from 63.72% to 66.54%, and genome sizes range between 4.39-5.18 Mb. Genes for salt tolerance and denitrification are distinguishing features that separate Denitromonas spp. from the closely related Azoarcus and Aromatoleum genera.

microbiology↗

bioRxiv2022

Coupling of NOD2 to GIV is Required for Bacterial Sensing

ABSTRACT/SUMMARYSensing of pathogens by Nucleotide oligomerization domain (NOD)-like 2 receptor (NOD2) induces a protective inflammatory response that coordinates bacterial clearance. Polymorphisms in NOD2 impair bacterial clearance, leading to chronic gut inflammation in Crohns disease (CD) via mechanisms that remain incompletely understood. We identify GIV/Girdin (CCDC88A) as a NOD2-interactor that shapes bacterial sensing-and-signaling in macrophages. Myeloid-specific GIV depletion exacerbated and protracted infectious colitis and abolished the protective effect of muramyl dipeptide (MDP) in both chemical colitis and severe sepsis. In the presence of GIV, macrophages enhance anti-bacterial pathways downstream of NOD2, clear microbes rapidly and concomitantly suppress inflammation. GIVs actions are mediated via its C-terminus, which directly binds the terminal leucine-rich repeat (LRR#10) of NOD2; binding is augmented by MDP and ATP, precedes receptor oligomerization, and is abolished by the 1007fs CD-risk variant which lacks LRR#10. Findings illuminate mechanisms that underlie protective NOD2 signaling and loss of function in the major 1007fs variant. In briefThis work reveals a mechanism by which macrophages use their innate immune sensor, NOD2, to protect the host against overzealous inflammation during bacterial infections, and the consequences of its loss, as occurs in the most important Crohns disease-risk variant. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/489574v2_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@139a1feorg.highwire.dtl.DTLVardef@ba5354org.highwire.dtl.DTLVardef@b4d933org.highwire.dtl.DTLVardef@11fe12e_HPS_FORMAT_FIGEXP M_FIG GRAPHIC ABSTRACT C_FIG HIGHLIGHTSO_LIGIV is a functional and direct interactor of the terminal LRR repeat of NOD2 C_LIO_LIMice lacking M[FE] GIV develop dysbiosis, protracted ileocolitis and sepsis C_LIO_LIMDP/NOD2-dependent protective host responses require GIV C_LIO_LICD-risk NOD2 1007fs variant lacking the terminal LRR#10 cannot bind GIV C_LI

immunology↗

bioRxiv2021

The minor spliceosome offers a therapeutically viable target for the treatment of a broad spectrum of cancers

Minor splicing is a second splicing system required for the correct expression of [~]700 human minor intron-containing genes (MIGs). Many MIGs are expressed in vigorously proliferating cells and are frequently dysregulated in cancer including BRAF, ERK, JNK and p38. Minor splicing is carried out by the minor spliceosome which comprises several unique components, including a 65kDa protein encoded by RNPC3. We show that Rnpc3 heterozygosity reduces tumour burden in a broad spectrum of in vivo cancer settings, without harming normal tissues. Using the collective power of zebrafish, mouse and human cancer models, we reveal a sequence of events connecting Rnpc3 deficiency and impaired splicing of MIGs to DNA damage and activation of a Tp53-dependent transcriptional program that restricts tumour burden by inducing cell cycle arrest and apoptosis. Interrogation of human liver and lung cancer transcriptomes curated in TCGA revealed that the expression of many of the genes encoding protein components of the minor spliceosome is upregulated in these cancers. This is accompanied by upregulation of the expression of MIGs that are enriched in cell cycle and DNA damage pathways. These findings suggest that cancer cells can invoke mechanisms to increase the efficiency of minor splicing to support their high proliferation rates. Finally, Kaplan Meier survival analysis shows that highly expressed MIGs are frequently associated with poor patient survival. Taken together, these results indicate that the minor spliceosome offers a therapeutically viable target for the treatment of a broad spectrum of cancers.

cancer biology↗

bioRxiv2021

Sulfate adenylyl transferase kinetics and mechanisms of metabolic inhibitors of microbial sulfate respiration

Sulfate analog oxyanions that function as selective metabolic inhibitors of dissimilatory sulfate reducing microorganisms (SRM) are widely used in ecological studies and industrial applications. As such, it is important to understand the mode of action and mechanisms of tolerance or adaptation to these compounds. Different oxyanions vary widely in their inhibitory potency and mechanism of inhibition, but current evidence suggests that the sulfate adenylyl transferase/ATP sulfurylase (Sat) enzyme is an important target. We heterologously expressed and purified the Sat from the model SRM, Desulfovibrio alaskensis G20. With this enzyme we determined the turnover kinetics (kcat, KM) for alternative substrates (molybdate, selenate, arsenate, monofluorophosphate, and chromate) and inhibition constants (KI) for competitive inhibitors (perchlorate, chlorate, and nitrate). These measurements enable the first quantitative comparisons of these compounds as substrates or inhibitors of a purified Sat from a respiratory sulfate reducer. We compare predicted half-maximal inhibitory concentrations (IC50) based on Sat kinetics with measured IC50 values against D. alaskensis G20 growth and discuss our results in light of known mechanisms of sensitivity or resistance to oxyanions. This analysis helps with the interpretation of recent adaptive laboratory evolution studies and illustrates the value of interpreting gene-microbe-environment interactions through the lens of enzyme kinetics.

microbiology↗

bioRxiv2020

Genetic and phylogenetic analysis of dissimilatory iodate-reducing bacteria identifies potential niches across the world's oceans

Iodine is oxidized and reduced as part of a biogeochemical cycle that is especially pronounced in the oceans, where the element naturally concentrates. The use of oxidized iodine in the form of iodate (IO3-) as an electron acceptor by microorganisms is poorly understood. Here, we outline genetic, physiological, and ecological models for dissimilatory IO3- reduction to iodide (I-) by a novel estuarine bacterium, Denitromonas iodocrescerans strain IR-12, sp. nov. Our results show that dissimilatory iodate reduction (DIR) by strain IR-12 is molybdenum-dependent and requires an IO3- reductase (idrA) and likely other genes in a mobile cluster with a conserved association across known and predicted DIR microorganisms (DIRM). Based on genetic and physiological data, IO3- is likely reduced to hypoiodous acid (HIO), which rapidly disproportionates into IO3- and iodide (I-), in a respiratory pathway that provides an energy yield equivalent to that of nitrate or perchlorate respiration. Consistent with the ecological niche expected of such a metabolism, idrA is enriched in the metagenome sequence databases of marine sites with a specific biogeochemical signature and diminished oxygen. Taken together, these data suggest that DIRM help explain the disequilibrium of the IO3-:I- concentration ratio above oxygen minimum zones and support a widespread iodine redox cycle mediated by microbiology.

microbiology↗

bioRxiv2020

The Diversity and Evolution of Microbial Dissimilatory Phosphite Oxidation

Phosphite is the most energetically favorable chemotrophic electron donor known, with a half-cell potential (E{degrees}) of -650 mV for the PO4 3-/PO3 3- couple. Since the discovery of microbial dissimilatory phosphite oxidation (DPO) in 2000, the environmental distribution, evolution, and diversity of DPO microorganisms (DPOM) has remained enigmatic and only two species have been identified. Here metagenomic sequencing of phosphite enriched microbial communities enabled the reconstruction and metabolic characterization of 21 novel DPOM. These DPOM spanned six classes of bacteria, including the Negativicutes, Desulfotomaculia, Synergistia, Syntrophia, Desulfobacteria and Desulfomonilia_A. Comparing the DPO genes from the genomes of enriched organisms to over 17,000 publicly available metagenomes revealed the global existence of this metabolism in diverse anoxic environments, including wastewaters, sediments, and subsurface aquifers. Despite their newfound environmental and taxonomic diversity, metagenomic analyses suggested that the typical DPOM is a chemolithoautotroph that occupies low-oxygen environments and specializes in phosphite oxidation coupled to CO2 reduction. Phylogenetic analyses indicated that the DPO genes form a highly conserved cluster that likely has ancient origins predating the split of monoderm and diderm bacteria. By coupling microbial cultivation strategies with metagenomics, these studies highlighted the unsampled metabolic versatility latent in microbial communities. We have uncovered the unexpected prevalence, diversity, biochemical specialization, and ancient origins of a unique metabolism central to the redox cycling of phosphorus, a primary nutrient on earth. Significance StatementGeochemical models of the phosphorus (P) cycle uniquely ignore microbial redox transformations. Yet phosphite is a reduced P source that has been detected in several environments at concentrations that suggest a contemporary P redox cycle. Microbial dissimilatory phosphite oxidation (DPO) converts soluble phosphite into phosphate, and a false notion of rarity has limited our understanding of its diversity and environmental distribution. Here we demonstrate that DPO is an ancient energy metabolism hosted by taxonomically diverse, autotrophic bacteria that exist globally throughout anoxic environments. DPO microorganisms are therefore likely to have provided bioavailable phosphate and fixed carbon to anoxic ecosystems throughout Earths history and continue to do so in contemporary environments.

microbiology↗

bioRxiv2018

Effects of green seaweed extract on Arabidopsis early development suggest roles for hormone signalling in plant responses to algal fertilisers

The growing population requires sustainable, environmentally-friendly crops. The plant growth-enhancing properties of algal extracts have suggested their use as biofertilisers. The mechanism(s) by which algal extracts affect plant growth are unknown.\n\nWe examined the effects of extracts from the common green seaweed Ulva intestinalis on germination and root development in the model land plant Arabidopsis thaliana. Ulva extract concentrations above 0.1% inhibited Arabidopsis germination and root growth. Ulva extract <0.1% stimulated root growth. All concentrations of Ulva extract inhibited lateral root formation. An abscisic-acid-insensitive mutant, abi1, showed altered sensitivity to germination- and root growth-inhibition inhibition. Ethylene- and cytokinin-insensitive mutants were partly insensitive to germination-inhibition. This suggests that different mechanisms mediate each effect of Ulva extract on early Arabidopsis development and that multiple hormones contribute to germination-inhibition.\n\nElemental analysis showed that Ulva contains high levels of Aluminium ions (Al3+). Ethylene and cytokinin have been suggested to function in Al3+-mediated root growth inhibition: our data suggest that if Ulva Al3+ levels inhibit root growth, this is via a novel mechanism. We suggest algal extracts should be used cautiously as fertilisers, as the inhibitory effects on early development may outweigh any benefits if the concentration of extract is too high.

plant biology↗

bioRxiv2018

ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks

Mutations in the ATM tumor suppressor confer hypersensitivity to DNA-damaging agents. To explore genetic resistance mechanisms, we performed genome-wide CRISPR-Cas9 screens in cells treated with the DNA topoisomerase poison topotecan. Thus, we establish that loss of terminal components of the non-homologous end-joining (NHEJ) machinery or the BRCA1-A complex specifically confers topotecan resistance to ATM-deficient cells. We show that hypersensitivity of ATM-mutant cells to topotecan or the poly-(ADP-ribose) polymerase inhibitor olaparib is due to delayed homologous recombination repair at DNA-replication-fork-associated double-strand breaks (DSBs), resulting in toxic NHEJ-mediated chromosome fusions. Accordingly, restoring legitimate repair in ATM-deficient cells, either by preventing NHEJ DNA ligation or by enhancing DSB-resection by BRCA1-A complex inactivation, markedly suppresses this toxicity. Our work suggests opportunities for patient stratification in ATM-deficient cancers and when using ATM inhibitors in the clinic, and identifies additional therapeutic vulnerabilities that might be exploited when such cancers evolve drug resistance.\n\nOne Sentence SummaryATM counteracts toxic NHEJ at broken replication forks

cell biology↗

bioRxiv2017

Detection of functional protein domains by unbiased genome-wide forward genetic screening

Genetic and chemo-genetic interactions have played key roles in elucidating the molecular mechanisms by which certain chemicals perturb cellular functions. Many studies have employed gene knockout collections or gene disruption/depletion strategies to identify routes for evolving resistance to chemical agents. By contrast, searching for point-mutational genetic suppressors that can identify separation- or gain-of-function mutations, has been limited even in simpler, genetically amenable organisms such as yeast, and has not until recently been possible in mammalian cell culture systems. Here, by demonstrating its utility in identifying suppressors of cellular sensitivity to the drugs camptothecin or olaparib, we describe an approach allowing systematic, large-scale detection of spontaneous or chemically-induced suppressor mutations in yeast and in haploid mouse embryonic stem cells in a short timeframe, and with potential applications in essentially any other haploid system. In addition to its utility for molecular biology research, this protocol can be used to identify drug targets and to predict mechanisms leading to drug resistance. Mapping suppressor mutations on the primary sequence or three-dimensional structures of protein suppressor hits provides insights into functionally relevant protein domains, advancing our molecular understanding of protein functions, and potentially helping to improve drug design and applicability.

molecular biology↗