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      A Model System for Studying the Transcriptomic and Physiological Changes Associated with Mammalian Host-Adaptation by Leptospira interrogans Serovar Copenhageni

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          Abstract

          Leptospirosis, an emerging zoonotic disease with worldwide distribution, is caused by spirochetes belonging to the genus Leptospira. More than 500,000 cases of severe leptospirosis are reported annually, with >10% of these being fatal. Leptospires can survive for weeks in suitably moist conditions before encountering a new host. Reservoir hosts, typically rodents, exhibit little to no signs of disease but shed large numbers of organisms in their urine. Transmission occurs when mucosal surfaces or abraded skin come into contact with infected urine or urine-contaminated water or soil. In humans, leptospires can cause a variety of clinical manifestations, ranging from asymptomatic or mild fever to severe icteric (Weil's) disease and pulmonary haemorrhage. Currently, little is known about how Leptospira persist within a reservoir host. Prior in vitro studies have suggested that leptospires alter their transcriptomic and proteomic profiles in response to environmental signals encountered during mammalian infection. However, no study has examined gene expression by leptospires within a mammalian host-adapted state. To obtain a more faithful representation of how leptospires respond to host-derived signals, we used RNA-Seq to compare the transcriptome of L. interrogans cultivated within dialysis membrane chambers (DMCs) implanted into the peritoneal cavities of rats with that of organisms grown in vitro. In addition to determining the relative expression levels of “core” housekeeping genes under both growth conditions, we identified 166 genes that are differentially-expressed by L. interrogans in vivo. Our analyses highlight physiological aspects of host adaptation by leptospires relating to heme uptake and utilization. We also identified 11 novel non-coding transcripts that are candidate small regulatory RNAs. The DMC model provides a facile system for studying the transcriptional and antigenic changes associated with mammalian host-adaption, selection of targets for mutagenesis, and the identification of previously unrecognized virulence determinants.

          Author Summary

          Leptospirosis, a global disease caused by the unusual bacterium Leptospira, is transmitted from animals to humans. Pathogenic species of Leptospira are excreted in urine from infected animals and can continue to survive in suitable environments before coming into contact with a new reservoir or accidental host. Leptospires have an inherent ability to survive a wide range of conditions encountered in nature during transmission and within mammals. However, we know very little about the regulatory pathways and gene products that promote mammalian host adaptation and enable leptospires to establish infection. In this study, we used a novel system whereby leptospires are cultivated in dialysis membrane chambers implanted into the peritoneal cavities of rats to compare the gene expression profiles of mammalian host-adapted and in vitro-cultivated organisms. In addition to providing a facile system for studying the transcriptional and physiologic changes leptospires undergo during mammalian infection, our data provide a rational basis for selecting new targets for mutagenesis.

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          Regulatory RNAs in bacteria.

          Bacteria possess numerous and diverse means of gene regulation using RNA molecules, including mRNA leaders that affect expression in cis, small RNAs that bind to proteins or base pair with target RNAs, and CRISPR RNAs that inhibit the uptake of foreign DNA. Although examples of RNA regulators have been known for decades in bacteria, we are only now coming to a full appreciation of their importance and prevalence. Here, we review the known mechanisms and roles of regulatory RNAs, highlight emerging themes, and discuss remaining questions.
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            Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.

            The genome of the bacterium Borrelia burgdorferi B31, the aetiologic agent of Lyme disease, contains a linear chromosome of 910,725 base pairs and at least 17 linear and circular plasmids with a combined size of more than 533,000 base pairs. The chromosome contains 853 genes encoding a basic set of proteins for DNA replication, transcription, translation, solute transport and energy metabolism, but, like Mycoplasma genitalium, it contains no genes for cellular biosynthetic reactions. Because B. burgdorferi and M. genitalium are distantly related eubacteria, we suggest that their limited metabolic capacities reflect convergent evolution by gene loss from more metabolically competent progenitors. Of 430 genes on 11 plasmids, most have no known biological function; 39% of plasmid genes are paralogues that form 47 gene families. The biological significance of the multiple plasmid-encoded genes is not clear, although they may be involved in antigenic variation or immune evasion.
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              CDD: conserved domains and protein three-dimensional structure

              CDD, the Conserved Domain Database, is part of NCBI’s Entrez query and retrieval system and is also accessible via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. CDD provides annotation of protein sequences with the location of conserved domain footprints and functional sites inferred from these footprints. Pre-computed annotation is available via Entrez, and interactive search services accept single protein or nucleotide queries, as well as batch submissions of protein query sequences, utilizing RPS-BLAST to rapidly identify putative matches. CDD incorporates several protein domain and full-length protein model collections, and maintains an active curation effort that aims at providing fine grained classifications for major and well-characterized protein domain families, as supported by available protein three-dimensional (3D) structure and the published literature. To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS Pathog
                PLoS Pathog
                plos
                plospath
                PLoS Pathogens
                Public Library of Science (San Francisco, USA )
                1553-7366
                1553-7374
                March 2014
                13 March 2014
                : 10
                : 3
                : e1004004
                Affiliations
                [1 ]Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut, United States of America
                [2 ]Department of Pediatrics, University of Connecticut Health Center, Farmington, Connecticut, United States of America
                [3 ]Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventative Medicine, Trinity College Dublin, Dublin, Ireland
                [4 ]School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
                [5 ]Department of Genetics, School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
                [6 ]Unidade de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
                [7 ]Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
                [8 ]Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
                Medical College of Wisconsin, United States of America
                Author notes

                The authors have declared that no competing interests exist.

                Conceived and designed the experiments: MJC JEN. Performed the experiments: MJC SKS AA DH KH AAG JEN. Analyzed the data: MJC SKS DH KH AAG JCDH JEN. Contributed reagents/materials/analysis tools: MJC SKS KH JCDH JEN. Wrote the paper: MJC SKS KH JCDH JEN.

                [¤]

                Current address: UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin, Belfield, Dublin, Ireland.

                Article
                PPATHOGENS-D-13-02800
                10.1371/journal.ppat.1004004
                3953431
                24626166
                7bcb5ecc-00c7-48f4-b745-997811826872
                Copyright @ 2014

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 25 October 2013
                : 1 February 2014
                Page count
                Pages: 19
                Funding
                This work was supported by NIH grants AI-29735 (AA and MJC), Science Foundation Ireland awards 05/YI/B696 (JN) and 08/IN.1/B2104 (JH) and Research Stimulus Fund (06/363 Department of Agriculture, Food & Marine, Ireland) (JN), and a Science without Borders fellowship from the Brazilian National Council for Scientific and Technological Development (AAG). DH is supported by Wellcome Trust Computational Infection Biology Ph.D. Programme. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology
                Microbiology
                Bacterial Pathogens
                Gram Negative
                Emerging Infectious Diseases
                Host-Pathogen Interaction
                Medical Microbiology
                Microbial Growth and Development
                Microbial Pathogens
                Microbial Physiology
                Medicine
                Infectious Diseases
                Bacterial Diseases
                Leptospirosis
                Neglected Tropical Diseases
                Leptospirosis
                Veterinary Science
                Veterinary Diseases
                Zoonotic Diseases
                Leptospirosis
                Veterinary Microbiology

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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