Joshua P Ramsay

• PhD (Genetics)
• Fellow at Curtin University

Tripartite integrative and conjugative elements (ICE³) are a novel form of ICE that exist as three separate DNA regions integrated within the genomes of Mesorhizobium spp. Prior to conjugative transfer the three ICE³ regions of M. ciceri WSM1271 ICEMcSym¹²⁷¹ combine and excise to form a single circular element. This assembly requires three coordina...

Conjugation is a dominant mechanism of horizontal gene transfer and substantially contributes to the plasticity and evolvability of prokaryotic genomes. The impact of conjugation on genetic flux extends well beyond self-transmissible conjugative elements, because non-conjugative 'mobilizable elements' utilize other elements' conjugative apparatus f...

Significance Integrative and conjugative elements (ICEs) are one of the most prevalent but least-characterized families of mobile genetic elements in bacteria. We identified a family of ICEs that exists as three separate parts integrated within the single chromosomes of symbiotic mesorhizobia. These “tripartite ICEs,” through a series of chromosoma...

Significance Integrative and conjugative elements (ICEs) facilitate horizontal transfer of multiple genetic determinants. Here we show that a programmed ribosomal frameshift (PRF) contributes to the regulation of ICE transfer. The low-frequency PRF fuses the coding sequences of two genes, resulting in a single-protein Frameshifted excision activato...

Staphylococcus aureus is a common cause of hospital, community and livestock-associated infections and is increasingly resistant to multiple antimicrobials. A significant proportion of antimicrobial-resistance genes are plasmid-borne, but only a minority of S. aureus plasmids encode proteins required for conjugative transfer or Mob relaxase protein...

Winged helix–turn–helix (wHTH) proteins are diverse DNA-binding proteins that often oligomerize on DNA and participate in DNA recombination and transcriptional regulation. wHTH recombination directionality factors (RDFs) associated with tyrosine recombinases, stimulate excision of prophage and integrative and conjugative elements (ICEs). RdfS is re...

Rhizobia are soil bacteria capable of establishing symbiosis within legume root nodules, where they reduce atmospheric N2 into ammonia and supply it to the plant for growth. Australian soils often lack rhizobia compatible with introduced agricultural legumes, so inoculation with exotic strains has become a common practice for over 50 years. While e...

Rhizobia are a diverse group of α- and β-proteobacteria that boost soil fertility by forming a nitrogen-fixing symbiosis with legumes, which is why legumes are grown in rotation with cereals in agriculture. Rhizobia that naturally populate Australian soils are largely incompatible with exotic agricultural legumes, therefore, compatible strains have...

In 2010 a single isolate of a trimethoprim-resistant multilocus sequence type 5, Panton–Valentine leucocidin-positive, community-associated methicillin-resistant Staphylococcus aureus (PVL-positive ST5 CA-MRSA), colloquially named WA121, was identified in northern Western Australia (WA). WA121 now accounts for ~14 % of all WA MRSA infections. To ga...

Horizontal gene transfer is tightly regulated in bacteria. Often only a fraction of cells become donors even when regulation of horizontal transfer is coordinated at the cell population level by quorum sensing. Here, we reveal the widespread 'domain of unknown function' DUF2285 represents an 'extended-turn' variant of the helix-turn-helix domain th...

Mesorhizobia are soil bacteria that establish nitrogen-fixing symbioses with various legumes. Novel symbiotic mesorhizobia frequently evolve following horizontal transfer of symbiosis-gene-carrying integrative and conjugative elements (ICESyms) to indigenous mesorhizobia in soils. Evolved symbionts exhibit a wide range in symbiotic effectiveness, w...

Pseudomonas aeruginosa is an opportunistic pathogen. Here, we report the isolation of four bacteriophages from wastewater. All four bacteriophages belong to the Myoviridae family. Kara-mokiny 8, 13, and 16 are of the Pbunavirus genus and have genomes between 65,527 and 66,420-bp. Boorn-mokiny 1 is of the Phikzvirus genus and has a 278,796-bp genome...

Engineering signalling between plants and microbes could be exploited to establish host‐specificity between plant‐growth promoting bacteria and target crops in the environment. We previously engineered rhizopine signalling circuitry facilitating exclusive signalling between rhizopine producing (RhiP) plants and model bacterial strains. Here, we con...

The recombination directionality factors from Mesorhizobium spp. (RdfS) are involved in regulating the excision and transfer of integrative and conjugative elements. Here, solution small-angle X-ray scattering, and crystallization and preliminary structure solution of RdfS from Mesorhizobium japonicum R7A are presented. RdfS crystallizes in space g...

Horizontal transfer of the integrative and conjugative element ICEMlSymR7A converts non-symbiotic Mesorhizobium spp. into nitrogen-fixing legume symbionts. Here, we discover subpopulations of Mesorhizobium japonicum R7A become epigenetically primed for quorum-sensing (QS) and QS-activated horizontal transfer. Isolated populations in this state term...

Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbiosis (ICESyms). Here, we document and compare the c...

Initially reported in Western Australia in the 1980s, community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has become a major cause of S. aureus infections globally. We report the complete genome sequences of three of the earliest CA-MRSA strains isolated from remote Australian Indigenous communities in the Kimberley region of...

Sequence type 1 (ST1) methicillin-resistant Staphylococcus aureus (MRSA) type IV[2B] has become one of the most common community-associated MRSA clones in Australia. We report the complete genome sequence of one of the earliest isolated Australian S. aureus ST1-MRSA-IV strains, WBG8287, isolated from an Indigenous Australian patient living in the r...

Burn injuries can cause traumatic and debilitating physical trauma, with burn wounds prone to bacterial infection. This study examined in vitro the effectiveness of the silver nanoparticle based antimicrobial dressing, Acticoat™, in combination with a range of antimicrobial compounds against Staphylococcus aureus and Pseudomonas aeruginosa and inve...

In Staphylococcus aureus, most multiresistance plasmids lack conjugation or mobilization genes for horizontal transfer. However, most are mobilizable due to carriage of origin-of-transfer (oriT) sequences mimicking those of conjugative plasmids related to pWBG749. pWBG749-family plasmids have diverged to carry five distinct oriT subtypes and non-co...

Rhizobia are soil bacteria capable of forming N2-fixing symbioses with legumes, with highly effective strains often selected in agriculture as inoculants to maximize symbiotic N2 fixation. When rhizobia in the genus Mesorhizobium have been introduced with exotic legumes into farming systems, horizontal transfer of symbiosis integrative and conjugat...

Antimicrobial resistance poses a significant threat to modern healthcare as it limits treatment options for bacterial infections, particularly impacting those with chronic conditions such as cystic fibrosis (CF). Viscous mucus accumulation in the lungs of individuals genetically predisposed to CF leads to recurrent bacterial infections, necessitati...

Mesorhizobium is a genus of soil bacteria, some isolates of which form an endosymbiotic relationship with diverse legumes of the Loteae tribe. The symbiotic genes of these mesorhizobia are generally carried on integrative and conjugative elements termed symbiosis islands (ICESyms). Mesorhizobium strains that nodulate Lotus spp. have been divided in...

Of 1,033 E. coli urinary tract infection isolates collected from females >12 years of age in Australia, in 2019, only two isolates were resistant to fosfomycin with an MIC >256 mg/L. Despite having different multilocus sequence types, the two isolates harboured an identical plasmid-encoded fosA4 gene. The fosA4 gene has previously been identified i...

Horizontal transfer of plasmids encoding antimicrobial-resistance and virulence determinants has been instrumental in Staphylococcus aureus evolution, including the emergence of community-associated methicillin-resistant S. aureus (CA-MRSA). In the early 1990s the first CA-MRSA isolated in Western Australia (WA), WA-5, encoded cadmium, tetracycline...

Staphylococcus aureus is a serious human and animal pathogen. Multilocus sequence type 612 (ST612) is the dominant methicillin-resistant S. aureus (MRSA) clone in certain South African hospitals and is sporadically isolated from horses and horse-associated veterinarians in Australia. Colonisation and infection by ST612-MRSA is increasing in Western...

Integrative and conjugative elements (ICEs) are chromosomally-integrated mobile genetic elements that excise from their host chromosome and transfer to other bacteria via conjugation. ICEMlSym R7A is the prototypical member of a large family of “symbiosis ICEs” which confer upon their hosts the ability to form a nitrogen-fixing symbiosis with a var...

The resurgence of whooping cough reflects novel genetic variants of Bordetella pertussis and inadequate protection conferred by current acellular vaccines (aP). Biofilm is a source of novel vaccine candidates, including membrane protein assembly factor (BamB) and lipopolysaccharide assembly protein (LptD). Responses of BALB/c mice to candidate vacc...

Staphylococcal Plasmids, Transposable and Integrative Elements, Page 1 of 2 Abstract Strains of Staphylococcus aureus, and to a lesser extent other staphylococcal species, are a significant cause of morbidity and mortality. An important factor in the notoriety of these organisms stems from their frequent resistance to many antimicrobial agents us...

We report here the complete genome sequence of Stenotrophomonas maltophilia AB550, a multidrug- and solar radiation-resistant strain isolated from the effluents of an urban wastewater treatment plant in Western Australia. The genome consists of a single 4.9-Mb chromosome.

Staphylococcus aureus is a serious pathogen of humans and animals. Multilocus sequence type 612 is dominant and highly virulent in South African hospitals but relatively uncommon elsewhere. We present the complete genome sequence of methicillin-resistant Staphylococcus aureus strain SVH7513, isolated from a horse at a veterinary clinic in New South...

Urban wastewater treatment plant effluents represent one of the major emission sources of antibiotic-resistant bacteria (ARB) in natural aquatic environments. In this study, the effect of artificial solar radiation on total culturable heterotrophic bacteria and ARB (including amoxicillin-resistant, ciprofloxacin-resistant, rifampicin-resistant, sul...

Predicted secondary structures of RdfG, RdfM, and RdfS. Secondary structures were predicted using Jpred(v4) [64]. α-helices are highlighted in yellow, β-sheets are highlighted in blue. All three proteins carry a predicted two stranded MerR-family winged helix-turn-helix motif characteristic of RDFs [25]. (TIF)

Production of AHLs by TraI1. The C. violaceum CV026 biosensor strain [29] was used to detect the production of AHLs in (A) E. coli DH10B or (B) M. loti R7ANS either constitutively expressing ICEMcSym1271-derived traI1 from the plasmid pPR3-traI1, or carry the empty vector pPR3. Production of a purple violacein halo indicated production of C4-C8 AHL...

TPM values and DESeq2 output for differential gene expression analysis. (XLSX)

TraI1-dependent activation of the traI1 promoter by TraR1 and TraR2. β-galactosidase assays [67] were performed on a set of R7ANS strains carrying the same traI1 promoter-lacZ fusion on either pSDz, pSDz-traR1, or pSDz-traR2. These strains were induced for expression of traR1/traR2 with 1 μM IPTG, and also carried either a constitutively expressed...

RNA-Seq mapping of the transcriptional start sites for traI1, traI2, and rdfS. The promoter regions of traI1 (A), traI2 (B), and rdfS genes (C) from WSM1271 were identified based on similarity with homologous regions in R7A. Nucleotide alignments were performed using the T-Coffee multiple sequence aligner [63]. Transcriptional start sites for R7A g...

Alignment of traI2 promoter regions and TraI2 protein sequences in diverse Mesorhizobium spp. (A) The nucleotide sequence of traI2 promoters and (B) the TraI2 amino acid sequences from six Mesorhizobium strains were aligned using the T-coffee multiple sequence aligner [63]. (TIF)

Possible evolution of QS loci on ICEMlSymR7A and ICEMcSym1271. On ICEMlSymR7A, traR is encoded upstream of an operon encoding the likely non-functional AHL-synthase gene traI2, msi172-msi171 and qseM-qseC. The functional AHL synthase TraI1 is encoded at a separate location. ICEMcSym1271 carries traR2 upstream of qseM-qseC, however, the traI2-msi172...

Oligonucleotides used in this study. (PDF)

Supplementary materials and methods. (DOCX)

The currently widespread and increasing prevalence of resistant bacterial pathogens is a significant medical problem. In clinical strains of staphylococci, the genetic determinants that confer resistance to antimicrobial agents are often located on mobile elements, such as plasmids. Many of these resistance plasmids are capable of horizontal transm...

Successful process development for the bioleaching of mineral ores, particularly the refractory copper sulfide ore chalcopyrite, remains a challenge in regions where freshwater is scarce and source water contains high concentrations of chloride ion. In this study, a pure isolate of Acidihalobacter prosperus strain F5 was characterized for its abili...

We report here the complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain WSM1497, the efficient nitrogen-fixing microsymbiont and commercial inoculant in Australia of the forage legume Biserrula pelecinus . The genome consists of 7.2 Mb distributed across a single chromosome (6.67 Mb) and a single plasmid (0.53 Mb).

Background Statins are a class of therapeutics used to regulate serum cholesterol and reduce the risk of heart disease. Although statins are highly effective in removing cholesterol from the blood, their consumption has been linked to potential adverse effects in some individuals. The most common events associated with statin intolerance are myopat...

Integrative and conjugative elements (ICEs) are generally regarded as regions of contiguous DNA integrated within a bacterial genome that are capable of excision and horizontal transfer via conjugation. We recently characterized a unique group of ICEs present in Mesorhizobium spp., which exist as three entirely separate but inextricably linked chro...

The use of halotolerant acidophiles for bioleaching provides a biotechnical approach for the extraction of metals from regions where high salinity exists in the ores and source water. Here, we describe the first draft genome of a new species of a halotolerant and iron- and sulfur-oxidizing acidophile, Acidihalobacter ferrooxidans DSM 14175 (strain...

The principal genomic features of Acidihalobacter prosperus DSM 14174 (strain V6) are presented here. This is a mesophilic, halotolerant, and iron/sulfur-oxidizing acidophile that was isolated from seawater at Vulcano, Italy. It has potential for use in biomining applications in regions where high salinity exists in the source water and ores.

Methicillin resistance in the clinically important bacterium Staphylococcus aureus (MRSA) has evolved in multiple S. aureus lineages through acquisition of chromosomally integrating mobile genetic elements named SCCmec. Now Rice and colleagues show that the conserved SCCmec cch gene encodes an active DNA helicase, thus suggesting that extrachromoso...

The horizontal gene transfer facilitated by mobile genetic elements impacts almost all areas of bacterial evolution, including the accretion and dissemination of antimicrobial-resistance genes in the human and animal pathogen Staphylococcus aureus. Genome surveys of staphylococcal plasmids have revealed an unexpected paucity of conjugation and mobi...

We report the complete genome sequence of Mesorhizobium ciceri strain CC1192, an efficient nitrogen-fixing microsymbiont of Cicer arietinum (chickpea). The genome consists of 6.94 Mb distributed between a single chromosome (6.29 Mb) and a plasmid (0.65 Mb).

We report the complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain WSM1284, a nitrogen-fixing microsymbiont of the pasture legume Biserrula pelecinus . The genome consists of 6.88 Mb distributed between a single chromosome (6.33 Mb) and a single plasmid (0.55 Mb).

Aspiration of bile into the cystic fibrosis (CF) lung has emerged as a prognostic factor for reduced microbial lung biodiversity and the establishment of often fatal, chronic pathogen infections. Staphylococcus aureus is one of the earliest pathogens detected in the lungs of children with CF, and once established as a chronic infection, strategies...

Importance: Understanding the mechanism of antimicrobial resistance transfer in bacteria such as Staphylococcus aureus is an important step toward potentially slowing the spread of antimicrobial resistant infections. This work establishes protein-DNA interactions essential for the transfer of the Staphylococcus aureus multiresistance plasmid pSK41...

Different modes of bacterial taxis play important roles in environmental adaptation, survival, colonization and the dissemination of disease. One mode of taxis is flotation due to the production of gas vesicles. Gas vesicles are proteinaceous intracellular organelles, permeable only to gas, that enable flotation in aquatic niches. Gene clusters for...

Random transposon mutagenesis is a powerful technique used to generate libraries of genetic insertions in many different bacterial strains. Here we develop a system facilitating random transposon mutagenesis in a range of different Gram-negative bacterial strains, including Pectobacterium atrosepticum, Citrobacter rodentium, Serratia sp. ATCC39006,...

Mobile genetic elements run an evolutionary gauntlet to maintain their mobility in the face of selection against their selfish dissemination but, paradoxically, they can accelerate the adaptability of bacteria through the gene-transfer events that they facilitate. These temporally conflicting evolutionary forces have shaped exquisite regulation sys...

The Mesorhizobium loti symbiosis island (ICEMlSymR7A) is a 500-kb mobile integrative and conjugative element (ICE) that converts non-symbiotic mesorhizobia into strains capable of forming a symbiosis with Lotus corniculatus. ICEMlSymR7A chromosomal excision and conjugative transfer is stimulated by the quorum-sensing regulator TraR. Quorum sensing...

To describe a family of conjugative plasmids isolated from colonizing community Staphylococcus aureus and determine their ability to mobilize unrelated antimicrobial resistance/virulence plasmids, not encoding mobilization functions. Plasmid pWBG749 was labelled with Tn551 (pWBG749e) to enable laboratory manipulation. Plasmid pWBG749e was conjugate...

Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous bacterial signalling molecule produced by diguanylate cyclases of the GGDEF-domain family. Elevated c-di-GMP levels or increased GGDEF protein expression is frequently associated with the onset of sessility and biofilm formation in numerous bacterial species. Conversely,...

A symbiosis island is a genomic island that confers upon the bacterium carrying it the ability to form a mutualistic relationship with a eukaryotic host. The symbiosis island of Mesorhizobium loti strain R7A is a 501.8-kb chromosomally integrated element that is able to excise and transfer by conjugation to nonsymbiotic mesorhizobia in the environm...

Serratia sp. strain ATCC 39006 is a Gram-negative bacterium and a member of the Enterobacteriaceae that produces various bioactive secondary metabolites, including the tripyrrole red pigment prodigiosin and the β-lactam antibiotic 1-carbapenen-2-em-3-carboxylic acid (a carbapenem). This strain is the only member of the Enterobacteriaceae known to n...

Serratia sp. ATCC 39006 (S39006) is a Gram-negative enterobacterium that is virulent in plant and animal models. It produces a red-pigmented trypyrrole secondary metabolite, prodigiosin (Pig), and a carbapenem antibiotic (Car), as well as the exoenzymes, pectate lyase and cellulase. Secondary metabolite production in this strain is controlled by a...

ICEMlSym(R7A) of Mesorhizobium loti is an integrative and conjugative element (ICE) that confers the ability to form a nitrogen-fixing symbiosis with Lotus species. Horizontal transfer is activated by TraR and N-acyl-homoserine lactone (AHL), which can stimulate ICE excision in 100% of cells. However in wild-type cultures, the ICE is excised at low...

Gas vesicles are gas-filled microcompartments produced by many cyanobacteria and haloarchaea to regulate buoyancy and control positioning in the water column. Recently we identified the first case of gas vesicle production by a member of the Enterobacteriaceae, Serratia sp ATCC39006. Gas vesicle production enabled colonisation of the air-liquid int...

Gas vesicles are hollow intracellular proteinaceous organelles produced by aquatic Eubacteria and Archaea, including cyanobacteria and halobacteria. Gas vesicles increase buoyancy and allow taxis toward air-liquid interfaces, enabling subsequent niche colonization. Here we report a unique example of gas vesicle-mediated flotation in an enterobacter...

Serratia sp. ATCC 39006 (S39006) is a Gram-negative bacterium that is virulent in plant (potato) and animal (Caenorhabditis elegans) models. It produces two secondary metabolite antibiotics, a prodigiosin and a carbapenem, and the exoenzymes, pectate lyase and cellulase. A complex regulatory network that includes quorum sensing (QS) controls produc...

The symbiosis island ICEMlSym(R7A) of Mesorhizobium loti R7A is an integrative and conjugative element (ICE) that carries genes required for a nitrogen-fixing symbiosis with Lotus species. ICEMlSym(R7A) encodes homologues (TraR, TraI1 and TraI2) of proteins that regulate plasmid transfer by quorum sensing in rhizobia and agrobacteria. Introduction...

The Mesorhizobium loti strain R7A symbiosis island is an Integrative Conjugative Element (ICE), herein termed ICEMlSymR7A, which integrates into a phetRNA gene. Integration reconstructs the phetRNA gene at one junction with the core chromosome, and a direct repeat of the 3-prime 17 bp of the gene is formed at the other junction. We show that the IC...

The imprinted gene and parent-of-origin effect database (www.otago.ac.nz/IGC) consists of two sections. One section catalogues the current literature on imprinted genes in humans and animals. The second, and new, section catalogues current reports of parental origin of de novo mutations in humans alone. The addition of a catalogue of de novo mutati...

Genomic imprinting, the parent-of-origin-specific silencing of a small proportion of genes, introduces a paradoxical vulnerability of hemizygosity into the diploid mammalian genome. To facilitate the evaluation of the biological and evolutionary significance of imprinting, we have collated a census of known imprinted genes, listing 83 transcription...