David Edward Whitworth

David Edward Whitworth
Aberystwyth University | AU · Institute of Biological, Environmental and Rural Sciences

PhD

About

106
Publications
8,561
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Introduction
Professor of Biochemistry at Aberystwyth University.. Currently researching myxobacterial social interactions using a variety of approaches - experimental (genetic/biochemical) and theoretical (bioinformatics/genomics).
Additional affiliations
January 2008 - December 2012
Aberystwyth University
January 2001 - December 2010
The University of Warwick

Publications

Publications (106)
Article
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Myxobacteria are fascinating and important prokaryotes. [...]
Article
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Biochemistry graduates need to be creative, however assessing creativity requires the production of novelty, judged by or against that of peers. A related phenomenon is ‘creative self‐efficacy’ (CSE) – one's self‐belief in producing creative outcomes. CSE is a contributor to creativity, but is more easily assessed, and thus more amenable for target...
Article
Full-text available
Myxobacteria are fascinating and complex microbes. They prey upon other members of the soil microbiome by secreting antimicrobial proteins and metabolites, and will undergo multicellular development if starved. The genome sequence of the model myxobacterium Myxococcus xanthus DK1622 was published in 2006 and 15 years later, 163 myxobacterial genome...
Article
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Two-component systems (TCSs) are ubiquitous signaling pathways, typically comprising a sensory histidine kinase (HK) and a response regulator, which communicate via intermolecular kinase-to-receiver domain phosphotransfer. Hybrid HKs constitute non-canonical TCS signaling pathways, with transmitter and receiver domains within a single protein commu...
Article
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Bacterial predation is a ubiquitous and fundamental biological process, which influences the community composition of microbial ecosystems. Among the best characterised bacterial predators are the myxobacteria, which include the model organism Myxococcus xanthus . Predation by M. xanthus involves the secretion of antibiotic metabolites and hydrolyt...
Article
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As prokaryotes diverge by evolution, essential ‘core’ genes required for conserved phenotypes are preferentially retained, while inessential ‘accessory’ genes are lost or diversify. We used the recently expanded number of myxobacterial genome sequences to investigate the conservation of their signalling proteins, focusing on two sister genera (Myxo...
Article
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Members of the predatory Myxococcales (myxobacteria) possess large genomes, undergo multicellular development, and produce diverse secondary metabolites, which are being actively prospected for novel drug discovery. To direct such efforts, it is important to understand the relationships between myxobacterial ecology, evolution, taxonomy, and genomi...
Article
Prokaryotic ncRNAs are important regulators of gene expression, and can be involved in complex signalling networks. The myxobacteria are model organisms for studies into multicellular development and microbial predation, being particularly renowned for their large genomes and exceptionally sophisticated signalling networks. However, apart from two...
Article
Myxobacteria are Gram-negative bacteria, notable for their predatory and antimicrobial activities, which dictate the outcomes of their interactions with neighbouring organisms. They are abundant and widespread in nature, and can significantly affect the microbiome of an environment. We hypothesise that there are underlying molecular mechanisms in p...
Chapter
The myxobacteria are an order of abundant and virtually ubiquitous soil-dwelling Deltaproteobacteria. They initially attracted scientific attention in the nineteenth century for their ability to aggregate when starved, cooperating as a population of cells to form multicellular fruiting bodies containing differentiated cell types. Later, it became a...
Article
Extracellular membrane vesicles are produced by all domains of life (bacteria, archaea and eukaryotes). Bacterial extracellular vesicles (outer membrane vesicles or OMVs) are produced by outer membrane blebbing, and contain proteins, nucleic acids, virulence factors, lipids and metabolites. OMV functions depend on their internal composition, theref...
Article
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Network analysis was used to show changes in network attributes by analyzing the relations among the main soil microbial groups in a potted tomato soil inoculated with arbuscular mycorrhizal fungus, treated with low doses of Mentha spicata essential oil, or both, and then exposed to tenfold higher oil addition (stress pulse). Pretreatments were cho...
Article
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Corallococcus is a genus of predators with broad prey ranges, whose genomes contain large numbers of gene clusters for secondary metabolite biosynthesis. The physiology and evolutionary heritage of eight Corallococcus species strains were characterized using a range of analyses and assays. Multiple metrics confirmed that each strain belonged to a n...
Article
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Despite widespread use in human biology, genome-wide association studies (GWAS) of bacteria are few and have, to date, focused primarily on pathogens. Myxobacteria are predatory microbes with large patchwork genomes, with individual strains secreting unique cocktails of predatory proteins and metabolites. We investigated whether a GWAS strategy cou...
Article
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For decades, myxobacteria have been spotlighted as exemplars of social “wolf‐pack” predation, communally secreting antimicrobial substances into the shared public milieu. This behavior has been described as cooperative, becoming more efficient if performed by more cells. However, laboratory evidence for cooperativity is limited and of little releva...
Article
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Rhodococcus sp.strain BUPNP1 can utilize the priority environmental pollutant 4-nitrophenol (4-NP) as its sole source of carbon and energy. In this study, genome and transcriptome sequencing were used to gain mechanistic insights into 4-NP degradation. The draft BUPNP1 genome is 5.56 Mbp and encodes 4,963 proteins, which are significantly enriched...
Data
Inoculum dependence of BUPNP1 growth and 4-NP consumption.
Data
Relative expression of BUPNP1 genes after 6 and 12 h in 4-NP or glucose. FPKM values, normalized for gene length.
Data
RAST annotation of CDS in the BUPNP1 genome.
Data
Comparison of the 4-NP biodegradation efficiencies reported for Rhodococcus strains.
Data
Differentially expressed BUPNP1 genes in 4-NP vs. glucose, after 6 and 12 h.
Article
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Corallococcus is an abundant genus of predatory soil myxobacteria, containing two species, C. coralloides (for which a genome sequence is available) and C. exiguus. To investigate the genomic basis of predation, we genome-sequenced 23 Corallococcus strains. Genomic similarity metrics grouped the sequenced strains into at least nine distinct genomos...
Data
16S rRNA gene sequence tree of newly sequenced and DSM Corallococcus strains, with other myxobacteria included as an outgroup.
Data
PhyloPhlAn phylogenetic tree of 400 gene sequences from the 24 genome-sequenced Corallococcus strains.
Data
EggNOG annotations of core and accessory genes for all 24 Corallococci, Group A Corallococci, Group B Corallococci and Myxococcus genomes. Sequences outputted from SPINE and used as inputs into EggNOG are also provided as separate rows in a further worksheet.
Data
Predation activity of Corallococcus strains against ten prey organisms (predation zone diameter 7 days after inoculation).
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OrthoFinder tree based on the presence/absence matrix of orthogroups amongst the 24 sequenced Corallococcus genomes.
Data
AntiSMASH predicted compound classes by genome and named compounds predicted to be synthesized by genome.
Article
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Predatory bacteria are able to kill and consume other microbes and are therefore of interest as potential sources of new antimicrobial substances for applications in the clinic. “Wolf pack” predators kill prey by secreting antimicrobial substances into their surroundings, and those substances can kill prey organisms independently of the predatory c...
Article
Predation is an extreme form of competition between bacteria, involving the secretion of antimicrobial substances by predators, often packaged within outer membrane vesicles (OMVs). Recent studies into the Myxococcus xanthus/Escherichia coli predator/prey relationship have illuminated transcriptional changes during predation, identifying likely tar...
Article
Full-text available
Predation is a fundamental ecological process, but within most microbial ecosystems the molecular mechanisms of predation remain poorly understood. We investigated transcriptome changes associated with the predation of Escherichia coli by the myxobacterium Myxococcus xanthus using mRNA sequencing. Exposure to pre-killed prey significantly altered e...
Data
Isolate classification and predation activity data.
Data
16S rRNA gene sequence distance tree of all isolates and selected type strains. The scale shows the per base substitution rate.
Data
16S rRNA gene sequence trees of Cluster 1 (Corallococcus spp.) and Cluster 2 (Myxococcus spp.) isolates. 16S rRNA gene sequences of the isolates are available through www.ncbi.nlm.nih.gov under accession references MF163277-MF163389.
Article
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Myxobacteria are natural predators of microorganisms and the subjects of concerted efforts to identify novel antimicrobial compounds. Myxobacterial predatory activity seems to require more than just the possession of specific antimicrobial metabolites. Thus a holistic approach to studying predation promises novel insights into antimicrobial action....
Article
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Motivation: Two-component systems (TCS) are the main signalling pathways of prokaryotes, and control a wide range of biological phenomena. Their functioning depends on interactions between TCS proteins, the specificity of which is poorly understood. Results: The MetaPred2CS web-server interfaces a sequence-based meta-predictor specifically desig...
Article
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Glacial ice surfaces represent a seasonally evolving three-dimensional photic zone which accumulates microbial biomass and potentiates positive feedbacks in ice melt. Since viruses are abundant in glacial systems and may exert controls on supraglacial bacterial production, we examined whether changes in resource availability would promote changes i...
Poster
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The rumen microbiome is diverse, containing bacteria, protozoa, fungi and archaea, whose function determines the ability of ruminants to convert otherwise undegradable plant fibre into a source of nutrients. It is becoming increasingly apparent that the production of membrane vesicles (MVs) is a ubiquitous cellular phenomenon. The aims of this stud...
Article
Laboratory-based practical classes are a common feature of life science teaching, during which students learn how to perform experiments and generate/interpret data. Practical classes are typically instructional, concentrating on providing topic- and technique-specific skills, however to produce research-capable graduates it is also important to de...
Data
Supplementary material 1 . Supplementary File 1: Tab-delimited spreadsheet detailing the composition of the cellular, OMV and soluble supernatant fractions from an M. xanthus culture (first worksheet), and the AA frequencies of the proteomes that we describe in the article (second worksheet)
Data
Supplementary material 2 . Supplementary File 2: Identification data for M. xanthus datasets. The number of peptides assigned to each protein, percentage coverage of each protein, and amount of each protein are presented as an average (first worksheet) of three replicates (subsequent worksheets)
Article
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Outer membrane vesicles (OMVs) shed from bacteria contribute to pathogenesis by promoting colonization of host tissues and trafficking virulence factors into host cells via fusion with the host cell plasma membrane. Glyeraldehyde-3-phosphate dehydrogenase (GAPDH) is also secreted by prokaryotes, but enhances pathogenesis by promoting adhesion of ba...
Article
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Two-component systems (TCSs) are abundant prokaryotic signaling pathways, whose evolution is of particular importance because of their role in bacterial pathogenicity. Comparative genomics can provide important insights into the evolution of these genes, but inferences are dependent on the relatedness of the compared genomes. This study investigate...
Article
We provide a prepackaged molecular biology course, which has a broad context and is scalable to large numbers of students. It is provided complete with technical setup guidance, a reliable assessment regime, and can be readily implemented without any development necessary. Framed as a forensic examination of blue/white cloning plasmids, the course...
Article
Full-text available
Background: Two component systems (TCS) are signalling complexes manifested by a histidine kinase (receptor) and a response regulator (effector). They are the most abundant signalling pathways in prokaryotes and control a wide range of biological processes. The pairing of these two components is highly specific, often requiring costly and time-con...
Article
Subsets of proteins involved in distinct functional processes are subject to different selective pressures. We investigated whether there is an amino acid composition bias (AACB) inherent in discrete subsets of proteins, and whether we could identify changing patterns of AACB during the life cycle of the social bacterium Myxococcus xanthus. We quan...
Article
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The P2CS database (http://www.p2cs.org/) is a comprehensive resource for the analysis of Prokaryotic Two-Component Systems (TCSs). TCSs are comprised of a receptor histidine kinase (HK) and a partner response regulator (RR) and control important prokaryotic behaviors. The latest incarnation of P2CS includes 164 651 TCS proteins, from 2758 sequenced...
Article
In science education, laboratory practicals are frequently assessed through submission of a report. A large increase in student numbers necessitated us adapting a traditional practical report into an online test with automated marking. The assessment was designed to retain positive features of the traditional laboratory report but with added pedago...
Article
The handshake is a commonplace greeting in many cultures, but it has the potential to transmit infectious organisms directly between individuals. We developed an experimental model to assay transfer of bacteria during greeting exchange, and show that transfer is dramatically reduced when engaging in alternative so-called dap greetings known as the...
Poster
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Biofilms are the predominant phenotype of microbes in nature, especially within the rumen1. Biofilms are often rich in bacterial-derived outer membrane vesicles (OMVs); structures ranging from 20 to 250 nm which play a role in defence and resistance, nutrient acquisition and signalling. Yet, the importance of OMVs in rumen remains unknown. In this...
Article
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Background Regulatory proteins (RPs) such as transcription factors (TFs) and two-component system (TCS) proteins control how prokaryotic cells respond to changes in their external and/or internal state. Identification and annotation of TFs and TCSs is non-trivial, and between-genome comparisons are often confounded by different standards in annotat...
Article
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Background Transcription factors (TFs) are DNA-binding proteins that regulate gene expression by activating or repressing transcription. Some have housekeeping roles, while others regulate the expression of specific genes in response to environmental change. The majority of TFs are multi-domain proteins, and they can be divided into families accord...
Data
Classification of TF categories: Schematic representation of the conserved domain architectures.
Data
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Classification of TF families: List of domain architectures.
Article
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The Deltaproteobacterium Myxococcus xanthus predates upon members of the soil microbial community by secreting digestive factors and lysing prey cells. Like other Gram-negative bacteria, M. xanthus produces outer membrane vesicles (OMVs), and we show here M. xanthus OMVs are able to kill cells of Escherichia coli. The OMVs of M. xanthus were found...
Chapter
Two-component systems (TCSs) are signalling pathways found abundantly in prokaryotes, and they are the dominant mechanism for stimulus-responsive adaptation in such organisms. An ever-increasing number of physiological phenomena are known to be regulated by TCSs, including cell cycle progression, pathogenesis, motility, and biofilm formation. The b...
Article
Outer membrane vesicles (OMVs) are produced from the outer membrane (OM) of myxobacterial cells and are found in large quantities within myxobacterial biofilms. It has been proposed that OMVs are involved in several of the social behaviors exhibited by the myxobacteria, including motility and predation. Proteomic data suggest that specific proteins...
Article
Full-text available
Two-component systems (TCSs) are modular and diverse signalling pathways, involving a stimulus-responsive transfer of phosphoryl groups from transmitter to partner receiver domains. TCS gene and domain organisation are both potentially informative regarding biological function, interaction partnerships and molecular mechanisms. However, there is cu...
Data
Numbers of TCS gene tetrads/triads/pairs/orphans per replicon. For every replicon analysed, the total number of HK, PP and RR genes are presented, along with the numbers of TCS genes found as orphans, paired genes, triads and tetrads. In addition the types of TCS genes found as orphans, and in various paired-gene geometries are provided.
Data
Dataset of TCS gene foci domain/gene organisation. A dataset of TCS gene foci, with each focus defined using the locus tag of the first gene in the focus. For each focus, gene architecture and domain organisation are presented.
Article
Myxobacterial development requires the coordinated action of both intracellular and intercellular signalling pathways. A dataset of myxobacterial developmental gene properties suggests that genes encoding components of intracellular pathways tend to be less conserved, yield less severe phenotypes upon deletion and lie closer to the chromosomal orig...
Article
Full-text available
P2CS (http://www.p2cs.org) is a specialized database for prokaryotic two-component systems (TCSs), virtually ubiquitous signalling proteins which regulate a wide range of physiological processes. The primary aim of the database is to annotate and classify TCS proteins from completely sequenced prokaryotic genomes and metagenomes. Information within...
Data
Converging stream formations. Fruiting body simulations begin with streams of cells converging to form an aggregate. To maintain cell density within the fruit, the initial stream formations are augmented with four cell influx regions, one at each boundary of the simulation (in the xy-plane). Cells are created at the influx regions and allowed to mo...
Data
Simulation of the effects of adhesion on stream formation. As adhesion becomes stronger cells cannot break apart and remain together in tighter clusters until the slime effectively becomes so viscous, cells cannot move. The head, tail and body of each cell are coloured red, blue and black respectively. Plots are a two-dimensional (xy-plane) top dow...