Marc R Wilkins

University of New South Wales, Kensington, New South Wales, Australia

Are you Marc R Wilkins?

Claim your profile

Publications (156)567.26 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Cancer cachexia is a systemic, paraneoplastic syndrome seen in patients with advanced cancer. There is growing interest in the altered muscle pathophysiology experienced by cachectic patients. This study reports the microarray analysis of gene expression in cardiac and skeletal muscle in the colon 26 carcinoma (C26) mouse model of cancer cachexia. A total of 268 genes were found to be differentially expressed in cardiac muscle tissue, compared to non-tumor bearing controls. This was smaller than the 1533 genes that changed in cachectic skeletal muscle. In addition to different numbers of genes changing, different cellular functions were seen to change in each tissue. The cachectic heart showed signs of inflammation, similar to cachectic skeletal muscle, but did not show the upregulation of ubiquitin-dependent protein catabolic processes or downregulation of genes involved in cellular energetics and muscle regeneration that characterizes skeletal muscle cachexia. qPCR was used to investigate a subset of inflammatory genes in the cardiac and skeletal muscle of independent cachectic samples; this revealed that B4galt1, C1s, Serpina3n and Vsig4 were significantly upregulated in cardiac tissue whereas C1s and Serpina3n were significantly upregulated in skeletal tissue. Our skeletal muscle microarray results were also compared to those from three published microarray studies, and found to be consistent in terms of the genes differentially expressed and the functional processes affected. Our study highlights that skeletal and cardiac muscles are affected differently in the C26 mouse model of cachexia and that therapeutic strategies cannot assume that both muscle types will show a similar response.
    Physiological Genomics 09/2015; DOI:10.1152/physiolgenomics.00128.2014 · 2.37 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Plant microRNAs (miRNAs) operate by guiding the cleavage or translational inhibition of mRNA targets. They act as key gene regulators for development and environmental adaptation, and Dicer-partnering proteins DRB1 and DRB2 govern which form of regulation plays the dominant role. Mutation of Drb1 impairs transcript cleavage whereas mutation of Drb2 ablates translational inhibition. Regulation of gene expression by miRNA-guided cleavage has been extensively studied but there is much less information about genes regulated through miRNA-mediated translation inhibition. Here we compared the proteomes of drb1 and drb2 mutants to gain insight into the indirect effect of the different miRNA regulatory mechanisms in Arabidopsis thaliana. Our results show that miRNAs operating through transcript cleavage regulate a broad spectrum of processes, including catabolism and anabolism, and this was particularly obvious in the fatty acid degradation pathway. Enzymes catalyzing each step of this pathway were upregulated in drb1. In contrast, DRB2-associated translational inhibition appears to be less ubiquitous and specifically aimed toward responses against abiotic or biotic stimuli.
    Journal of Proteome Research 09/2015; DOI:10.1021/acs.jproteome.5b00616 · 4.25 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Nutritional therapy is well established as a means to induce remission in active Crohn's disease (CD). Evidence indicates that exclusive enteral nutrition (EEN) therapy for CD both alters the intestinal microbiota and directly suppresses the inflammatory response in the intestinal mucosa. However, the pathway(s) through which EEN suppresses inflammation is still unknown. Therefore, the aim of the current study was to use microarray technology to investigate the major pathway by which polymeric formula (PF) alters inflammatory processes in epithelial cells in vitro. HT-29 cells were grown to confluence and then co-cultured with tumour necrosis factor (TNF)-α (100 ng/ml) for 5 h in the presence or absence of PF, as used for EEN. Following incubation, RNA was extracted and subjected to polymerase chain reaction (PCR) and microarray analysis. Enzyme-linked immunosorbent assays were employed to evaluate cytokine protein levels. Neither TNF-α nor PF had a toxic effect on cells over the experimental period. Microarray analysis showed that PF modulated the expression of genes specifically linked to nuclear factor (NF)-κB, resulting in downregulation of a number of genes in this pathway. These findings were further confirmed by real-time PCR of selected dysregulated genes as well as reduced expression of IL-6 and IL-8 proteins following PF treatment. The results arising from this study provide evidence that PF alters the inflammatory responses in intestinal epithelial cells through modulation of the NF-κB pathway.
    Genes & Nutrition 09/2015; 10(5):479. DOI:10.1007/s12263-015-0479-x · 2.79 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Human bone marrow-derived stromal (skeletal) stem cells (BM-hMSC) are being employed in an increasing number of clinical trials for tissue regeneration. A limiting factor for their clinical use is the inability to obtain sufficient cell numbers. Human embryonic stem cells (hESC) can provide an unlimited source of clinical grade cells for therapy. We have generated MSC-like cells from hESC (called here hESC-stromal) that exhibit surface markers and differentiate to osteoblasts and adipocytes, similar to BM-hMSC. In the present study, we used microarray analysis to compare the molecular phenotype of hESC-stromal and immortalised BM-hMSC cells (hMSC-TERT). Of the 7379 genes expressed above baseline, only 9.3% of genes were differentially expressed between undiffer-entiated hESC-stromal and BM-hMSC. Following ex vivo osteoblast induction, 665 and 695 genes exhibited ≥2-fold change (FC) in hESC-stromal and BM-hMSC, respectively with 172 genes common to both cell types. Functional annotation of significantly changing genes revealed similarities in gene ontology between the two cell types. Interestingly, genes in categories of cell adhesion/motility and epithelial–mesenchymal transition (EMT) were highly enriched in hESC-stromal whereas genes associated with cell cycle processes were enriched in hMSC-TERT. This data suggests that while hESC-stromal cells exhibit a similar molecular phenotype to hMSC-TERT, differences exist that can be explained by ontological differences between these two cell types. hESC-stromal cells can thus be considered as a possible alternative candidate cells for hMSC, to be employed in regen-erative medicine protocols.
  • [Show abstract] [Hide abstract]
    ABSTRACT: The Hmt1 methyltransferase is the predominant arginine methyltransferase in Saccharomyces cerevisiae. There are 18 substrate proteins described for this methyltransferase, however native sites of methylation have only been identified on two of these proteins. Here we used peptide immunoaffinity enrichment, followed by LC-ETD-MS/MS, to discover 21 native sites of arginine methylation on 5 putative Hmt1 substrate proteins, namely Gar1p (H/ACA ribonucleoprotein complex subunit 1), Nop1p (rRNA 2'-O-methyltransferase fibrillarin), Npl3p (nucleolar protein 3), Nsr1p (nuclear localization sequence-binding protein), and Rps2p (40S ribosomal protein S2). The sites, many of which were found to be mono- or di-methylated, were predominantly found in RGG (Arg-Gly-Gly) motifs. Heavy methyl-SILAC validated the majority of these peptides. The above proteins, and relevant sites of methylation, were subsequently validated by in vitro methylation with recombinant Hmt1. This brings the total of Hmt1 substrate proteins for which native methylation sites have been identified to five. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 06/2015; 15(18). DOI:10.1002/pmic.201500075 · 3.81 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The Wollemi pine (Wollemia nobilis) is a rare Southern conifer with striking morphological similarity to fossil pines. A small population of W. nobilis was discovered in 1994 in a remote canyon system in the Wollemi National Park (near Sydney, Australia). This population contains fewer than 100 individuals and is critically endangered. Previous genetic studies of the Wollemi pine have investigated its evolutionary relationship with other pines in the family Araucariaceae, and have suggested that the Wollemi pine genome contains little or no variation. However, these studies were performed prior to the widespread use of genome sequencing, and their conclusions were based on a limited fraction of the Wollemi pine genome. In this study, we address this problem by determining the entire sequence of the W. nobilis chloroplast genome. A detailed analysis of the structure of the genome is presented, and the evolution of the genome is inferred by comparison with the chloroplast sequences of other members of the Araucariaceae and the related family Podocarpaceae. Pairwise alignments of whole genome sequences, and the presence of unique pseudogenes, gene duplications and insertions in W. nobilis and Araucariaceae, indicate that the W. nobilis chloroplast genome is most similar to that of its sister taxon Agathis. However, the W. nobilis genome contains an unusually high number of repetitive sequences, and these could be used in future studies to investigate and conserve any remnant genetic diversity in the Wollemi pine.
    PLoS ONE 06/2015; 10(6):e0128126. DOI:10.1371/journal.pone.0128126 · 3.23 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Human proteome analysis now requires an understanding of protein isoforms. We recently published the PG Nexus pipeline, which facilitates high confidence validation of exons and splice junctions by integrating genomics and proteomics data. Here we comprehensively explore how RNA-seq transcriptomics data, and proteomic analysis of the same sample, can identify protein isoforms. RNA-seq data from human mesenchymal (hMSC) stem cells were analysed with our new TranscriptCoder tool to generate a database of protein isoform sequences. MS/MS data from matching hMSC samples were then matched against the TranscriptCoder-derived database, along with Ensembl and the neXtProt database. Querying the TranscriptCoder-derived or Ensembl database could unambiguously identify ~450 protein isoforms, with isoform-specific proteotypic peptides, including candidate hMSC-specific isoforms for the genes DPYSL2 and FXR1. Where isoform-specific peptides did not exist, groups of non-isoform-specific proteotypic peptides could specifically identify many isoforms. In both the above cases, isoforms will be detectable with targeted MS/MS assays. Unfortunately, our analysis also revealed that some isoforms will be difficult to identify unambiguously as they do not have peptides that are sufficiently distinguishing. We co-visualise mRNA isoforms and peptides in a genome browser to illustrate the above situations. Mass spectrometry data is available via ProteomeXchange (PXD001449).
    Journal of Proteome Research 05/2015; 14(9). DOI:10.1021/pr5011394 · 4.25 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: In recent years, protein methylation has been established as a major intracellular post-translational modification (PTM). It has also been proposed to modulate protein-protein interactions (PPIs) in the interactome. To investigate the effect of PTMs on PPIs, we recently developed the conditional two-hybrid (C2H) system. With this, we demonstrated that arginine methylation can modulate PPIs in the yeast interactome. Here, we used the C2H system to investigate the effect of lysine methylation. Specifically, we asked whether Ctm1p-mediated trimethylation of yeast cytochrome c Cyc1p, on lysine 78, modulates its interactions with Erv1p, Ccp1p, Cyc2p and Cyc3p. We show that the interactions between Cyc1p and Erv1p, and between Cyc1p and Cyc3p, are significantly increased upon trimethylation of lysine 78. This increase of interaction helps explain the reported facilitation of Cyc1p import into the mitochondrial intermembrane space upon methylation. This first application of the C2H system to the study of methyllysine-modulated interactions further confirms its robustness and flexibility. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 03/2015; 15(13). DOI:10.1002/pmic.201400521 · 3.81 Impact Factor
  • 02/2015; 1(3):14027. DOI:10.1038/nplants.2014.27
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The tephritid fruit flies include a number of economically important pests of horticulture, with a large accumulated body of research on their biology and control. Amongst the Tephritidae, the genus Bactrocera, containing over 400 species, presents various species groups of potential utility for genetic studies of speciation, behaviour or pest control. In Australia, there exists a triad of closely-related, sympatric Bactrocera species which do not mate in the wild but which, despite distinct morphologies and behaviours, can be force-mated in the laboratory to produce fertile hybrid offspring. To exploit the opportunities offered by genomics, such as the efficient identification of genetic loci central to pest behaviour and to the earliest stages of speciation, investigators require genomic resources for future investigations. We produced a draft de novo genome assembly of Australia's major tephritid pest species, Bactrocera tryoni. The male genome (650 -700 Mbp) includes approximately 150Mb of interspersed repetitive DNA sequences and 60Mb of satellite DNA. Assessment using conserved core eukaryotic sequences indicated 98% completeness. Over 16,000 MAKER-derived gene models showed a large degree of overlap with other Dipteran reference genomes. The sequence of the ribosomal RNA transcribed unit was also determined. Unscaffolded assemblies of B. neohumeralis and B. jarvisi were then produced; comparison with B. tryoni showed that the species are more closely related than any Drosophila species pair. The similarity of the genomes was exploited to identify 4924 potentially diagnostic indels between the species, all of which occur in non-coding regions. This first draft B. tryoni genome resembles other dipteran genomes in terms of size and putative coding sequences. For all three species included in this study, we have identified a comprehensive set of non-redundant repetitive sequences, including the ribosomal RNA unit, and have quantified the major satellite DNA families. These genetic resources will facilitate the further investigations of genetic mechanisms responsible for the behavioural and morphological differences between these three species and other tephritids. We have also shown how whole genome sequence data can be used to generate simple diagnostic tests between very closely-related species where only one of the species is scaffolded.
    BMC Genomics 12/2014; 15(1):1153. DOI:10.1186/1471-2164-15-1153 · 3.99 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Pathogenic species within the Campylobacter genus are responsible for a considerable burden on global health. Campylobacter concisus is an emergent pathogen that plays a role in acute and chronic gastrointestinal disease. Despite ongoing research on Campylobacter virulence mechanisms, little is known regarding the immunological profile of the host response to Campylobacter infection. In this study, we describe a comprehensive global profile of innate immune responses to C. concisus infection in differentiated THP-1 macrophages infected with an adherent and invasive strain of C. concisus. Using RNA-seq, qPCR, mass spectrometry and confocal microscopy, we observed differential expression of pattern recognition receptors and robust upregulation of DNA and RNA sensing molecules. In particular, we observed IFI16 inflammasome assembly in C. concisus-infected macrophages. Global profiling of the transcriptome revealed the significant regulation of a total of 8,343 transcripts upon infection with C. concisus, which included the activation of key inflammatory pathways involving CREB1, NF-κB, STAT and IRF signaling. Thirteen microRNAs and 333 non-coding RNAs were significantly regulated upon infection, including MIR221 which has been associated with colorectal carcinogenesis. This study represents a major advance in our understanding of host recognition and innate immune responses to infection by C. concisus. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
    Infection and Immunity 12/2014; 83(2). DOI:10.1128/IAI.03012-14 · 3.73 Impact Factor
  • Source
    Daniel L Winter · Melissa A Erce · Marc R Wilkins
    [Show abstract] [Hide abstract]
    ABSTRACT: Many proteins, including p53, the FoxO transcription factors, RNA polymerase II, pRb and the chaperones, have extensive post-translational modifications (PTMs). Many of these modifications modulate protein-protein interactions, controlling interaction presence / absence and specificity. Here we propose the notion of the interaction code; a widespread means by which modifications are used to control interactions in the proteome. Minimal interaction codes are likely to exist on proteins that have two or more modifications on an interaction interface and two or more interaction partners. By contrast, complex interaction codes are likely to be found on 'date hub' proteins that have many interactions, many PTMs, and/or are targeted by many modifying and demodifying enzymes. Proteins with new interaction codes should be discoverable by examining protein interaction networks, annotated with PTMs and protein modifying enzyme-substrate links. Multiple instances or combinations of phosphorylation, acetylation, methylation, O-GlcNAc and/or ubiquitination will likely form interaction codes, especially when co-located on a protein's single interaction interface. A network-based example of code discovery is given, predicting the yeast protein Npl3p to have a methylation / phosphorylation dependent interaction code.
    Journal of Proteome Research 10/2014; 13(12). DOI:10.1021/pr500585p · 4.25 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Sphingosine kinase 1 (SK1) is a signaling enzyme that catalyses the formation of sphingosine-1-phosphate. Overexpression of SK1 is causally associated with breast cancer progression and resistance to therapy. SK1 inhibitors are currently being investigated as promising breast cancer therapies. Two major transcriptional isoforms SK143kDa and SK151kDa have been identified, however the 51kDa variant is predominant in breast cancer cells. No studies have investigated the protein-protein interactions of the 51kDa isoform, and whether the two SK1 isoforms differ significantly in their interactions. Seeking an understanding of the regulation and role of SK1, we employed a triple-labeling SILAC-based (stable isotope-labeling by amino acids in cell culture) approach to identify SK1-interacting proteins common and unique to both isoforms. Of approximately 850 quantified proteins in SK1 immunoprecipitates, a high-confidence list of 30 protein interactions with each SK1 isoform was generated via meta-analysis of multiple experimental replicates. Many of the novel identified SK1 interaction partners such as supervillin, drebrin, and the MARCKS-related protein supported and highlighted previously-implicated roles of SK1 in breast cancer cell migration, adhesion, and cytoskeletal remodeling. Of these interactions several were found to be exclusive to the 43kDa isoform of SK1, including the PP2A phosphatase, a previously identified SK1-interacting protein. Other proteins such as allograft inflammatory factor 1-like protein, the latent-transforming growth factor beta-binding protein and dipeptidyl peptidase 2, were found to associate exclusively with the 51kDa isoform of SK1. In this report, we have identified common and isoform-specific SK1-interacting partners that provide insight into the molecular mechanisms that drive SK1-mediated oncogenicity.
    Molecular Endocrinology 09/2014; 28(11):me20131423. DOI:10.1210/me.2013-1423 · 4.02 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The koala, Phascolarctos cinereus, is a biologically unique and evolutionarily distinct Australian arboreal marsupial. The goal of this study was to sequence the transcriptome from several tissues of two geographically separate koalas, and to create the first comprehensive catalog of annotated transcripts for this species, enabling detailed analysis of the unique attributes of this threatened native marsupial, including infection by the koala retrovirus. RNA-Seq data was generated from a range of tissues from one male and one female koala and assembled de novo into transcripts using Velvet-Oases. Transcript abundance in each tissue was estimated. Transcripts were searched for likely protein-coding regions and a non-redundant set of 117,563 putative protein sequences was produced. In similarity searches there were 84,907 (72%) sequences that aligned to at least one sequence in the NCBI nr protein database. The best alignments were to sequences from other marsupials. After applying a reciprocal best hit requirement of koala sequences to those from tammar wallaby, Tasmanian devil and the gray short-tailed opossum, we estimate that our transcriptome dataset represents approximately 15,000 koala genes. The marsupial alignment information was used to look for potential gene duplications and we report evidence for copy number expansion of the alpha amylase gene, and of an aldehyde reductase gene. Koala retrovirus (KoRV) transcripts were detected in the transcriptomes. These were analysed in detail and the structure of the spliced envelope gene transcript was determined. There was appreciable sequence diversity within KoRV, with 233 sites in the KoRV genome showing small insertions/deletions or single nucleotide polymorphisms. Both koalas had sequences from the KoRV-A subtype, but the male koala transcriptome has, in addition, sequences more closely related to the KoRV-B subtype. This is the first report of a KoRV-B-like sequence in a wild population. This transcriptomic dataset is a useful resource for molecular genetic studies of the koala, for evolutionary genetic studies of marsupials, for validation and annotation of the koala genome sequence, and for investigation of koala retrovirus. Annotated transcripts can be browsed and queried at
    BMC Genomics 09/2014; 15(1):786. DOI:10.1186/1471-2164-15-786 · 3.99 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Here we describe the discovery of S. cerevisiae protein YJR129Cp as a new eukaryotic seven-beta-strand lysine methyltransferase. An immunoblotting screen of 21 putative methyltransferases showed a loss in the methylation of elongation factor 2 (EF2) on knockout of YJR129C. Mass spectrometric analysis of EF2 tryptic peptides localized this loss of methylation to lysine 509, in peptide LVEGLKR. In vitro methylation, using recombinant methyltransferases and purified EF2, validated YJR129Cp as responsible for methylation of lysine 509 and Efm2p as responsible for methylation at lysine 613. Contextualised on previously described protein structures, both sites of methylation were found at the interaction interface between EF2 and the 40S ribosomal subunit. In line with the recently discovered Efm1 and Efm2 we propose that YJR129C be named elongation factor methyltransferase 3 (Efm3). The human homolog of Efm3 is likely to be the putative methyltransferase FAM86A, according to sequence homology and multiple lines of literature evidence.
    Biochemical and Biophysical Research Communications 07/2014; 451(2). DOI:10.1016/j.bbrc.2014.07.110 · 2.30 Impact Factor
  • Natalie A Twine · Li Chen · Chi N Pang · Marc R Wilkins · Moustapha Kassem
    [Show abstract] [Hide abstract]
    ABSTRACT: The phenotype of osteoblastic (OB) cells in culture is currently defined using a limited number of markers of low sensitivity and specificity. For the clinical use of human skeletal (stromal, mesenchymal) stem cells (hMSC) in therapy, there is also a need to identify a set of gene markers that predict in vivo bone forming capacity. Thus, we used RNA sequencing to examine changes in expression for a set of skeletally-related genes across 8 time points between 0-12 days of ex vivo OB differentiation of hMSC. We identified 123 genes showing significant temporal expression change. Hierarchical clustering and Pearson's correlation generated 4 groups of genes: early stage differentiation genes (peak expression: 0-24hrs, n=28) which were enriched for extracellular matrix organisation, e.g. COL1A1, LOX, SERPINH1; middle stage differentiating genes (peak expression days: 3 and 6, n=20) which were enriched for extracellular matrix/skeletal system development e.g. BMP4, CYP24A1, TGFBR2; and late stage differentiation genes (peak expression days: 9 and 12, n=27) which were enriched for bone development/osteoblast differentiation, e.g. BMP2, IGF2. In addition, we identified 13 genes with bimodal temporal expression (2 peaks of expression: day 0 and 12) including VEGFA, PDGFA and FGF2. We examined the specificity of the 123 genes' expression in skeletal tissues and thus propose a set of ex vivo differentiation-stage-specific markers (n=21). In an independent analysis, we identified a subset of genes (n=20, e.g. ELN, COL11A1, BMP4) to predict the bone forming capacity of hMSC and another set (n=20, e.g. IGF2, TGFB2, SMAD3) associated with the ex vivo phenotype of hMSC obtained from osteoporotic patients.
    Bone 06/2014; 67. DOI:10.1016/j.bone.2014.06.027 · 3.97 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Full text available at: The koala (Phascolarctos cinereus) is an iconic Australian animal. Koalas are both biologically unique and evolutionarily distinct as the only living representative of the marsupial family Phascolarctidae. Their unique and highly specific diet of eucalyptus leaves, combined with the increasing threats of predation and habitat loss through urbanisation, mean that koalas are particularly vulnerable to the deleterious effects of fragmented habitat and population bottlenecks. They are further threatened by disease such as Chlamydia and there is increasing interest in the varying strains of the Koala Retrovirus. We present preliminary transcriptome and genome data for the koala and introduce the Koala Genome Consortium (KGC), a group working towards the production of a high quality draft assembly of the koala genome. The KGC is currently comprised of several Australian research institutes and Universities although our intention is to recruit researchers from around the world to contribute to the genome assembly and annotation process and ultimately make use of the assembled genome. Once available as an annotated draft, we anticipate the genome sequence will add significant value to the extensive body of existing research for koalas.
    05/2014; 24:91-92. DOI:10.3853/j.1835-4211.24.2014.1624
  • [Show abstract] [Hide abstract]
    ABSTRACT: This is the story of the experience of a multidisciplinary group at Macquarie University in Sydney as we participated in, and impacted upon, major currents that washed through protein science as the field of Proteomics emerged. The large scale analysis of proteins became possible. This is not a history of the field. Instead we have tried to encapsulate the stimulating personal ride we had transiting from conventional academe, to a Major National Research Facility, to the formation of Proteomics company Proteome Systems Ltd. There were lots of blind alleys, wrong directions, but we also got some things right and our efforts, along with those of many other groups around the world, did change the face of protein science. While the transformation is by no means yet complete, protein science is very different from the field in the 1990's. This article is part of a Special Issue entitled: 20years of Proteomics.
    Journal of proteomics 04/2014; 107. DOI:10.1016/j.jprot.2014.04.006 · 3.89 Impact Factor
  • Source
    Mangala A Nadkarni · Zhiliang Chen · Marc R Wilkins · Neil Hunter
    [Show abstract] [Hide abstract]
    ABSTRACT: The human oral microbiome has a major role in oral diseases including dental caries. Our studies on progression of caries infection through dentin and more recently, the invasion of vital dental pulp, detected Lactobacillus rhamnosus in the initial stages of infection of vital pulp tissue. In this study employing current high-throughput next generation sequencing technology we sought to obtain insight into genomic traits of tissue invasive L. rhamnosus, to recognise biomarkers that could provide an understanding of pathogenic potential of lactobacilli, generally regarded as safe. Roche GS FLX+ technology was used to generate whole genome sequences of two clinical isolates of L. rhamnosus infecting vital pulp. Detailed genome-wide comparison of the genetic profiles of tissue invasive L. rhamnosus with probiotic L. rhamnosus was performed to test the hypothesis that specific strains of L. rhamnosus possessing a unique gene complement are selected for the capacity to invade vital pulp tissue. Analysis identified 264 and 258 genes respectively, from dental pulp-invasive L. rhamnosus strains LRHMDP2 and LRHMDP3 isolated from two different subjects that were not present in the reference probiotic L. rhamnosus strain ATCC 53103 (GG). Distinct genome signatures identified included the presence of a modified exopolysaccharide cluster, a characteristic confirmed in a further six clinical isolates. Additional features of LRHMDP2 and LRHMDP3 were altered transcriptional regulators from RpoN, NtrC, MutR, ArsR and zinc-binding Cro/CI families, as well as changes in the two-component sensor kinase response regulator and ABC transporters for ferric iron. Both clinical isolates of L. rhamnosus contained a single SpaFED cluster, as in L. rhamnosus Lc705, instead of the two Spa clusters (SpaCBA and SpaFED) identified in L. rhamnosus ATCC 53103 (GG). Genomic distance analysis and SNP divergence confirmed a close relationship of the clinical isolates but segregation from the reference probiotic L. rhamnosus strain ATCC 53103 (GG).
    PLoS ONE 03/2014; 9(3):e90643. DOI:10.1371/journal.pone.0090643 · 3.23 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Post-translational lysine methylation is well established as a regulator of histone activity; however it is emerging that these modifications are also likely to play extensive roles outside of the histone code. Here we obtain new insights into non-histone lysine methylation and protein lysine methyltransferase (PKMT) activity by elucidating absolute stoichiometries of lysine methylation, using mass spectrometry and absolute quantification (AQUA), in wild-type and 5 PKMT gene deletion strains of Saccharomyces cerevisiae. By analyzing 8 sites of methylation in 3 non-histone proteins - elongation factor 1-α (EF1α), elongation factor 2 (EF2) and 60S ribosomal protein L42-A/B (Rpl42ab) - we find that: production of preferred methylation states on individual lysine residues is commonplace, and likely occurs through processive PKMT activity; Class I PKMTs can be associated with processive methylation; lysine residues are selectively methylated by specific PKMTs; and lysine methylation exists over a broad range of stoichiometries. Together these findings suggest that specific sites and forms of lysine methylation may play specialized roles in the regulation of non-histone protein activity. We also uncover new relationships between two proteins previously characterized as PKMTs, SEE1 and EFM1, in EF1α methylation, and show that past characterizations of EFM1 as having direct PKMT activity may require reinterpretation.
    Journal of Proteome Research 02/2014; 13(3). DOI:10.1021/pr401251k · 4.25 Impact Factor

Publication Stats

9k Citations
567.26 Total Impact Points


  • 1995–2015
    • University of New South Wales
      • School of Biotechnology and Biomolecular Sciences (BABS)
      Kensington, New South Wales, Australia
  • 2013
    • University of South Wales
      Понтиприте, Wales, United Kingdom
  • 1995–2012
    • Macquarie University
      • • Department of Chemistry and Biomolecular Sciences
      • • Department of Biological Sciences
      • • Australian Proteome Analysis Facility (APF)
      Sydney, New South Wales, Australia
  • 2011
    • University of Sydney
      Sydney, New South Wales, Australia
  • 2008
    • Johns Hopkins University
      Baltimore, Maryland, United States
  • 2007
    • Ruhr-Universität Bochum
      Bochum, North Rhine-Westphalia, Germany
  • 1996–2000
    • University of Geneva
      • • Department of Periodontology and Oral Physiopathology
      • • Department of Biochemistry
      Genève, Geneva, Switzerland
  • 1997
    • University of Liverpool
      Liverpool, England, United Kingdom