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Dineen RL, Penno C, Kelleher P, Bourin MJB, O'Connell‐Motherway M, van Sinderen D. Molecular analysis of the replication functions of the bifidobacterial conjugative megaplasmid pMP7017. Microb Biotechnol 2021; 14:1494-1511. [PMID: 33939264 PMCID: PMC8313286 DOI: 10.1111/1751-7915.13810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/22/2021] [Indexed: 11/29/2022] Open
Abstract
pMP7017 is a conjugative megaplasmid isolated from the gut commensal Bifidobacterium breve JCM7017 and was shown to encode two putative replicases, designated here as RepA and RepB. In the current work, RepB was identified as the pMP7017 replicative initiator, as the repB gene, and its surrounding region was shown to be sufficient to allow autonomous replication in two bifidobacterial species, B. breve and Bifidobacterium longum subsp. longum. RepB was shown to bind to repeat sequence downstream of its coding sequence and this region was determined to be essential for efficient replication. Based on our results, we hypothesize that pMP7017 is an iteron-regulated plasmid (IRP) under strict auto-regulatory control. Recombinantly produced and purified RepB was determined to exist as a dimer in solution, differing from replicases of other IRPs, which exist as a mix of dimers and monomers. Furthermore, a stable low-copy Bifidobacterium-E. coli shuttle vector, pRD1.3, was created which can be employed for cloning and expression of large genes, as was demonstrated by the cloning and heterologous expression of the 5.1 kb apuB gene encoding the extracellular amylopullulanase from B. breve UCC2003 into B. longum subsp. longum NCIMB8809.
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Affiliation(s)
- Rebecca L. Dineen
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
| | - Christophe Penno
- CNRS UMR 6553 EcoBioUniversite de Rennes 1Campus de Beaulieu, Bat. 14ARennes cedex35042France
| | - Philip Kelleher
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
| | - Maxence J. B. Bourin
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
| | | | - Douwe van Sinderen
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
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A Resource for Cloning and Expression Vectors Designed for Bifidobacteria: Overview of Available Tools and Biotechnological Applications. Methods Mol Biol 2021. [PMID: 33649956 DOI: 10.1007/978-1-0716-1274-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2023]
Abstract
Bifidobacteria represent an important group of (mostly) commensal microorganisms, which have enjoyed increasing scientific and industrial attention due to their purported health-promoting attributes. For the latter reason, several species have been granted "generally recognized as safe" (GRAS) and "qualified presumption of safety" (QPS) status by the Food and Drugs Administration (FDA) and European Food Safety Authority (EFSA) organizations. Increasing scientific evidence supports their potential as oral delivery vectors to produce bioactive and therapeutic molecules at intestinal level. In order to achieve an efficient utilization of bifidobacterial strains as health-promoting (food) ingredients, it is necessary to provide evidence on the molecular mechanisms behind their purported beneficial and probiotic traits, and precise mechanisms of interaction with their human (or other mammalian) host. In this context, developing appropriate molecular tools to generate and investigate recombinant strains is necessary. While bifidobacteria have long remained recalcitrant to genetic manipulation, a wide array of Bifidobacterium-specific replicating vectors and genetic modification procedures have been described in literature. The current chapter intends to provide an updated overview on the vectors used to genetically modify and manipulate bifidobacteria, including their general characteristics, reviewing examples of their use to successfully generate recombinant bifidobacterial strains for specific purposes, and providing a general workflow and cautions to design and conduct heterologous expression in bifidobacteria. Knowledge gaps and fields of research that may help to widen the molecular toolbox to improve the functional and technological potential of bifidobacteria are also discussed.
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Engineer probiotic bifidobacteria for food and biomedical applications - Current status and future prospective. Biotechnol Adv 2020; 45:107654. [DOI: 10.1016/j.biotechadv.2020.107654] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/14/2020] [Accepted: 11/01/2020] [Indexed: 12/15/2022]
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Park MJ, Park MS, Ji GE. Improvement of electroporation-mediated transformation efficiency for a Bifidobacterium strain to a reproducibly high level. J Microbiol Methods 2018; 159:112-119. [PMID: 30529116 DOI: 10.1016/j.mimet.2018.11.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 02/07/2023]
Abstract
Bifidobacteria are representative probiotics which are defined as live microorganisms that confer a health benefit on the host. Because of their safety and healthfulness when applied to humans, bifidobacteria are suitable as genetically engineered bacteria for applications to benefit human physiology and pathology. However, molecular biological studies of bifidobacteria have been limited due to insufficient genetic tools including effective transformation methods. The aim of this study is to improve the electroporation-mediated transformation efficiency of bifidobacteria to a reproducibly high level. The crucial factors that determine electroporation efficiency are the restriction-modification system, together with the cell wall and cell membrane structure of the bacteria. We optimized the bifidobacterial electroporation conditions by focusing on these factors as well as the amount of plasmid DNA used, the electrical parameters and the bacterial growth phase. As a result, the electroporation efficiency of B. bifidum BGN4 drastically and consistently increased from 103 to 105 CFU / μg DNA. The most significant factor for increasing the electroporation efficiency was the cell wall weakening mediated by NaCl, which improved the electroporation frequency by 20 times. Because the optimized electrotransformation conditions reported here should be widely applicable to other Bifidobacterium species, these could promote the extensive genetic manipulation of the various Bifidobacterium species in future studies.
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Affiliation(s)
- Min Ju Park
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Myeong Soo Park
- Research Center, BIFIDO Co., Ltd, Hongcheon 205-804, Republic of Korea; Department of Hotel Culinary Arts, Yeonsung University, Anyang 430-749, Republic of Korea.
| | - Geun Eog Ji
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 151-742, Republic of Korea; Research Center, BIFIDO Co., Ltd, Hongcheon 205-804, Republic of Korea.
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Stevens MJ, Venturini A, Lacroix C, Meile L. Enhancing oxidative stress resistance in Bifidobacterium thermophilum using a novel overexpression vector and transformation protocol. Plasmid 2017; 92:43-48. [DOI: 10.1016/j.plasmid.2017.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/09/2017] [Accepted: 06/09/2017] [Indexed: 12/30/2022]
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Cui Y, Hu T, Qu X, Zhang L, Ding Z, Dong A. Plasmids from Food Lactic Acid Bacteria: Diversity, Similarity, and New Developments. Int J Mol Sci 2015; 16:13172-202. [PMID: 26068451 PMCID: PMC4490491 DOI: 10.3390/ijms160613172] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/09/2015] [Accepted: 05/22/2015] [Indexed: 12/24/2022] Open
Abstract
Plasmids are widely distributed in different sources of lactic acid bacteria (LAB) as self-replicating extrachromosomal genetic materials, and have received considerable attention due to their close relationship with many important functions as well as some industrially relevant characteristics of the LAB species. They are interesting with regard to the development of food-grade cloning vectors. This review summarizes new developments in the area of lactic acid bacteria plasmids and aims to provide up to date information that can be used in related future research.
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Affiliation(s)
- Yanhua Cui
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Tong Hu
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin 150010, China.
| | - Lanwei Zhang
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Zhongqing Ding
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Aijun Dong
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
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Guglielmetti S, Mayo B, Álvarez-Martín P. Mobilome and genetic modification of bifidobacteria. Benef Microbes 2013; 4:143-66. [PMID: 23271067 DOI: 10.3920/bm2012.0031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Until recently, proper development of molecular studies in Bifidobacterium species has been hampered by growth difficulties, because of their exigent nutritive requirements, oxygen sensitivity and lack of efficient genetic tools. These studies, however, are critical to uncover the cross-talk between bifidobacteria and their hosts' cells and to prove unequivocally the supposed beneficial effects provided through the endogenous bifidobacterial populations or after ingestion as probiotics. The genome sequencing projects of different bifidobacterial strains have provided a wealth of genetic data that will be of much help in deciphering the molecular basis of the physiological properties of bifidobacteria. To this end, the purposeful development of stable cloning and expression vectors based on robust replicons - either from temperate phages or resident plasmids - is still needed. This review addresses the current knowledge on the mobile genetic elements of bifidobacteria (prophages, plasmids and transposons) and summarises the different types of vectors already available, together with the transformation procedures for introducing DNA into the cells. It also covers recent molecular studies performed with such vectors and incipient results on the genetic modification of these organisms, establishing the basis that would allow the use of bifidobacteria for future biotechnological applications.
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Affiliation(s)
- S Guglielmetti
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Sezione di Microbiologia Industriale, Università degli studi di Milano, Via Celoria 2, 20133 Milan, Italy
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Takahata M, Toh H, Nakano A, Takagi M, Murakami M, Ishii Y, Takizawa T, Tanabe S, Morita H. Complete sequence analysis of two cryptic plasmids from Bifidobacterium kashiwanohense JCM 15439 (type strain) isolated from healthy infant feces. Anim Sci J 2013; 85:158-63. [PMID: 23865717 DOI: 10.1111/asj.12095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 04/18/2013] [Indexed: 11/26/2022]
Abstract
Bifidobacterial plasmids reported so far are derived from a limited number of strains and plasmids of bifidobacterial type strains isolated from humans are unknown. We found that Bifidobacterium kashiwanohense JCM 15439 (type strain) isolated from a healthy infant contained two cryptic plasmids, designated pBBKW-1 and pBBKW-2. We determined and analyzed the complete sequences of both plasmids. pBBKW-1 (7716 bp) was predicted to replicate by a rolling-circle mechanism and encode six protein-coding genes, two of which are putative replication proteins. pBBKW-1 seems to be a cointegrate plasmid containing two copies of the plasmid pMG1 from Bifidobacterium longum. pBBKW-2 (2920 bp) was predicted to encode six protein-coding genes and be a theta-type replicating plasmid, which has been reported to be more stable than a rolling circle-type replicating plasmid frequently found in bifidobacteria. Our finding will provide new insights into safe recombinant plasmid constructions for humans.
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Affiliation(s)
- Muneaki Takahata
- School of Veterinary Medicine, Azabu University, Sagamihara; BioBank Co., Ltd, Okayama
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Ruiz L, Motherway MO, Lanigan N, van Sinderen D. Transposon mutagenesis in Bifidobacterium breve: construction and characterization of a Tn5 transposon mutant library for Bifidobacterium breve UCC2003. PLoS One 2013; 8:e64699. [PMID: 23737995 PMCID: PMC3667832 DOI: 10.1371/journal.pone.0064699] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/17/2013] [Indexed: 01/20/2023] Open
Abstract
Bifidobacteria are claimed to contribute positively to human health through a range of beneficial or probiotic activities, including amelioration of gastrointestinal and metabolic disorders, and therefore this particular group of gastrointestinal commensals has enjoyed increasing industrial and scientific attention in recent years. However, the molecular mechanisms underlying these probiotic mechanisms are still largely unknown, mainly due to the fact that molecular tools for bifidobacteria are rather poorly developed, with many strains lacking genetic accessibility. In this work, we describe the generation of transposon insertion mutants in two bifidobacterial strains, B. breve UCC2003 and B. breve NCFB2258. We also report the creation of the first transposon mutant library in a bifidobacterial strain, employing B. breve UCC2003 and a Tn5-based transposome strategy. The library was found to be composed of clones containing single transposon insertions which appear to be randomly distributed along the genome. The usefulness of the library to perform phenotypic screenings was confirmed through identification and analysis of mutants defective in D-galactose, D-lactose or pullulan utilization abilities.
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Affiliation(s)
- Lorena Ruiz
- Department of Microbiology and Alimentary Pharmabiotic Centre, National University of Ireland, Cork, Ireland
| | - Mary O’Connell Motherway
- Department of Microbiology and Alimentary Pharmabiotic Centre, National University of Ireland, Cork, Ireland
| | - Noreen Lanigan
- Department of Microbiology and Alimentary Pharmabiotic Centre, National University of Ireland, Cork, Ireland
| | - Douwe van Sinderen
- Department of Microbiology and Alimentary Pharmabiotic Centre, National University of Ireland, Cork, Ireland
- * E-mail:
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Carbohydrate stress-related response in Bifidobacterium pseudolongum subsp. globosum. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0432-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Accessing the inaccessible: molecular tools for bifidobacteria. Appl Environ Microbiol 2012; 78:5035-42. [PMID: 22582076 DOI: 10.1128/aem.00551-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bifidobacteria are an important group of the human intestinal microbiota that have been shown to exert a number of beneficial probiotic effects on the health status of their host. Due to these effects, bifidobacteria have attracted strong interest in health care and food industries for probiotic applications and several species are listed as so-called "generally recognized as safe" (GRAS) microorganisms. Moreover, recent studies have pointed out their potential as an alternative or supplementary strategy in tumor therapy or as live vaccines. In order to study the mechanisms by which these organisms exert their beneficial effects and to generate recombinant strains that can be used as drug delivery vectors or live vaccines, appropriate molecular tools are indispensable. This review provides an overview of the currently available methods and tools to generate recombinant strains of bifidobacteria. The currently used protocols for transformation of bifidobacteria, as well as replicons, selection markers, and determinants of expression, will be summarized. We will further discuss promoters, terminators, and localization signals that have been used for successful generation of expression vectors.
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12
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Cronin M, Zomer A, Fitzgerald GF, van Sinderen D. Identification of iron-regulated genes of Bifidobacterium breve UCC2003 as a basis for controlled gene expression. Bioeng Bugs 2012; 3:157-67. [PMID: 22179149 DOI: 10.4161/bbug.18985] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Iron is an essential growth factor for virtually all organisms. However, iron is not readily available in most environments and microorganisms have evolved specialized mechanisms, such as the use of siderophores and high-affinity transport systems, to acquire iron when confronted with iron-limiting conditions. In general these systems are tightly regulated to prevent iron-induced toxicity and because they are quite costly to the microbe. Because of this tight regulation we chose to explore the response of Bifidobacterium breve UCC2003 to iron limitation. Through microarray and complementation analyses we identified and characterized a presumed ferrous iron uptake system, encoded by bfeUOB, from B. breve UCC2003 and exploited its regulated transcription to develop an inducible expression system for use in bifidobacteria.
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Affiliation(s)
- Michelle Cronin
- Alimentary Pharmabiotic Centre and Department of Microbiology, University College Cork, Cork, Ireland
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de Lima Procópio RE, Araújo WL, Andreote FD, Azevedo JL. Characterization of a small cryptic plasmid from endophytic Pantoea agglomerans and its use in the construction of an expression vector. Genet Mol Biol 2011; 34:103-9. [PMID: 21637551 PMCID: PMC3085353 DOI: 10.1590/s1415-47572010005000096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Accepted: 07/15/2010] [Indexed: 11/22/2022] Open
Abstract
A circular cryptic plasmid named pPAGA (2,734 bp) was isolated from Pantoea agglomerans strain EGE6 (an endophytic bacterial isolate from eucalyptus). Sequence analysis revealed that the plasmid has a G+C content of 51% and contains four potential ORFs, 238(A), 250(B), 131(C), and 129(D) amino acids in length without homology to known proteins. The shuttle vector pLGM1 was constructed by combining the pPAGA plasmid with pGFPmut3.0 (which harbors a gene encoding green fluorescent protein, GFP), and the resulting construct was used to over-express GFP in E. coli and P. agglomerans cells. GFP production was used to monitor the colonization of strain EGE6gfp in various plant tissues by fluorescence microscopy. Analysis of EGE6gfp colonization showed that 14 days after inoculation, the strain occupied the inner tissue of Eucalyptus grandis roots, preferentially colonizing the xylem vessels of the host plants.
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Cronin M, Ventura M, Fitzgerald GF, van Sinderen D. Progress in genomics, metabolism and biotechnology of bifidobacteria. Int J Food Microbiol 2011; 149:4-18. [PMID: 21320731 DOI: 10.1016/j.ijfoodmicro.2011.01.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 01/06/2011] [Accepted: 01/10/2011] [Indexed: 12/16/2022]
Abstract
Members of the genus Bifidobacterium were first described over a century ago and were quickly associated with a healthy intestinal tract due to their numerical dominance in breast-fed babies as compared to bottle-fed infants. Health benefits elicited by bifidobacteria to its host, as supported by clinical trials, have led to their wide application as probiotic components of health-promoting foods, especially in fermented dairy products. However, the relative paucity of genetic tools available for bifidobacteria has impeded development of a comprehensive molecular understanding of this genus. In this review we present a summary of current knowledge on bifidobacterial metabolism, classification, physiology and genetics and outline the currently available methods for genetically accessing and manipulating the genus.
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Affiliation(s)
- Michelle Cronin
- Cork Cancer Research Centre, Mercy University Hospital and Leslie C. Quick Jnr. Laboratory, University College Cork, Cork, Ireland
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Abstract
Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments.
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Affiliation(s)
- Ju-Hoon Lee
- Department of Food Science and Nutrition, Microbial and Plant Genomics Institute, University of Minnesota, 1500 Gortner Ave., St. Paul, Minnesota 55108
| | - Daniel J. O'Sullivan
- Department of Food Science and Nutrition, Microbial and Plant Genomics Institute, University of Minnesota, 1500 Gortner Ave., St. Paul, Minnesota 55108
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Bottacini F, Medini D, Pavesi A, Turroni F, Foroni E, Riley D, Giubellini V, Tettelin H, van Sinderen D, Ventura M. Comparative genomics of the genus Bifidobacterium. MICROBIOLOGY-SGM 2010; 156:3243-3254. [PMID: 20634238 DOI: 10.1099/mic.0.039545-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Whole-genome sequencing efforts have revolutionized the study of bifidobacterial genetics and physiology. Unfortunately, the sequence of a single genome does not provide information on bifidobacterial genetic diversity and on how genetic variability supports improved adaptation of these bacteria to the environment of the human gastrointestinal tract (GIT). Analysis of nine genomes from bifidobacterial species showed that such genomes display an open pan-genome structure. Mathematical extrapolation of the data indicates that the genome reservoir available to the bifidobacterial pan-genome consists of more than 5000 genes, many of which are uncharacterized, but which are probably important to provide adaptive abilities pertinent to the human GIT. We also define a core bifidobacterial gene set which will undoubtedly provide a new baseline from which one can examine the evolution of bifidobacteria. Phylogenetic investigation performed on a total of 506 orthologues that are common to nine complete bifidobacterial genomes allowed the construction of a Bifidobacterium supertree which is largely concordant with the phylogenetic tree obtained using 16S rRNA genes. Moreover, this supertree provided a more robust phylogenetic resolution than the 16S rRNA gene-based analysis. This comparative study of the genus Bifidobacterium thus presents a foundation for future functional analyses of this important group of GIT bacteria.
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Affiliation(s)
- Francesca Bottacini
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland.,Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy
| | | | - Angelo Pavesi
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy
| | - Elena Foroni
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy
| | - David Riley
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Vanessa Giubellini
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy
| | - Hervé Tettelin
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy
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O'Connell Motherway M, O'Driscoll J, Fitzgerald GF, Van Sinderen D. Overcoming the restriction barrier to plasmid transformation and targeted mutagenesis in Bifidobacterium breve UCC2003. Microb Biotechnol 2008; 2:321-32. [PMID: 21261927 PMCID: PMC3815753 DOI: 10.1111/j.1751-7915.2008.00071.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In silico analysis of the Bifidobacterium breve UCC2003 genome predicted two distinct loci, which encode three different restriction/modification systems, each comprising a modification methylase and a restriction endonuclease. Based on sequence homology and observed protection against restriction we conclude that the first restriction endonuclease, designated BbrI, is an isoschizomer of BbeI, the second, BbrII, is a neoschizomer of SalI, while the third, BbrIII, is an isoschizomer of PstI. Expression of each of the B. breve UCC2003 methylase‐encoding genes in B. breve JCM 7017 established that BbrII and BbrIII are active and restrict incoming DNA. By exploiting knowledge on restriction/modification in B. breve UCC2003 we successfully increased the transformation efficiency to a level that allows the reliable generation of mutants by homologous recombination using a non‐replicative plasmid.
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Affiliation(s)
- Mary O'Connell Motherway
- Alimentary Pharmabiotic Centre, Department of Microbiology and Department of Food and Nutritional Sciences , National University of Ireland, Cork, Western Road, Cork, Ireland
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Cronin M, Sleator RD, Hill C, Fitzgerald GF, van Sinderen D. Development of a luciferase-based reporter system to monitor Bifidobacterium breve UCC2003 persistence in mice. BMC Microbiol 2008; 8:161. [PMID: 18816375 PMCID: PMC2564955 DOI: 10.1186/1471-2180-8-161] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Accepted: 09/24/2008] [Indexed: 12/12/2022] Open
Abstract
Background Probiotics such as bifidobacteria have been shown to maintain a healthy intestinal microbial balance and help protect against infections. However, despite these benefits, bifidobacteria still remain poorly understood at the biochemical, physiological and especially the genetic level. Herein we describe, for the first time, the development of a non-invasive luciferase-based reporter system for real-time tracking of Bifidobacterium species in vivo. Results The reporter vector pLuxMC1 is based on the recently described theta-type plasmid pBC1 from B. catenatulatum [1] and the luxABCDE operon from pPL2lux [2]. Derivatives of pLuxMC1, harbouring a bifidobacterial promoter (pLuxMC2) as well as a synthetically derived promoter (pLuxMC3) [3] placed upstream of luxABCDE, were constructed and found to stably replicate in B. breve UCC2003. The subsequent analysis of these strains allowed us to assess the functionality of pLuxMC1 both in vitro and in vivo. Conclusion Our results demonstrate the potential of pLuxMC1 as a real-time, non-invasive reporter system for Bifidobacterium. It has also allowed us, for the first time, to track the colonisation potential and persistence of this probiotic species in real time. An interesting and significant outcome of the study is the identification of the caecum as a niche environment for B. breve UCC2003 within the mouse gastrointestinal tract (GI) tract.
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Affiliation(s)
- Michelle Cronin
- Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland.
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Shkoporov AN, Efimov BA, Khokhlova EV, Steele JL, Kafarskaia LI, Smeianov VV. Characterization of plasmids from human infant Bifidobacterium strains: sequence analysis and construction of E. coli-Bifidobacterium shuttle vectors. Plasmid 2008; 60:136-48. [PMID: 18652842 DOI: 10.1016/j.plasmid.2008.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 06/26/2008] [Accepted: 06/27/2008] [Indexed: 11/29/2022]
Abstract
A survey of infant fecal Bifidobacterium isolates for plasmid DNA revealed that a significant portion of the strains, 17.6%, carry small plasmids. The majority of plasmid-harboring strains belonged to the Bifidobacterium longum/infantis group. Most of the plasmids could be assigned into two groups based on their sizes and the restriction profiles. Three plasmids, pB44 (3.6 kb) from B. longum, pB80 (4.9 kb) from Bifidobacterium bifidum, and pB21a (5.2kb) from Bifidobacterium breve were sequenced. While the former two plasmids were found to be highly similar to previously characterized rolling-circle replicating pKJ36 and pKJ56, respectively, the third plasmid, pB21a, does not share significant nucleotide homology with known plasmids. However, it might be placed into the pCIBb1-like group of bifidobacterial rolling-plasmids based on the homology of its Rep protein and the overall molecular organization. Two sets of Escherichia coli-Bifidobacterium shuttle vectors constructed based on pB44 and pB80 replicons were capable of transforming B. bifidum and B. breve strains with efficiency up to 3x10(4)cfu/microg DNA. Additionally, an attempt was made to employ a broad host range conjugation element, RP4, in developing of E. coli-Bifidobacterium gene transfer system.
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Affiliation(s)
- Andrei N Shkoporov
- Department of Microbiology, Russia State Medical University, Moscow, Russia
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Improved cloning vectors for bifidobacteria, based on the Bifidobacterium catenulatum pBC1 replicon. Appl Environ Microbiol 2008; 74:4656-65. [PMID: 18539807 DOI: 10.1128/aem.00074-08] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study reports the development of several cloning vectors for bifidobacteria based on the replicon of pBC1, a cryptic plasmid from Bifidobacterium catenulatum L48 thought to replicate via the theta mode. These vectors, in which antibiotic resistance genes encoding either erythromycin or tetracycline resistance acted as selection markers, were able to replicate in a series of eight Bifidobacterium species at frequencies ranging from 4.0 x 10(1) to 1.0 x 10(5) transformants microg(-1) but not in Lactococcus lactis or Lactobacillus casei. They showed a relative copy number of around 30 molecules per chromosome equivalent and a good segregational stability, with more than 95% of the cells retaining the vectors after 80 to 100 generations in the absence of selection. Vectors contain multiple cloning sites of different lengths, and the lacZalpha peptide gene was introduced into one of the molecules, thus allowing the easy selection of colonies harboring recombinant plasmids in Escherichia coli. The functionality of the vectors for engineering Bifidobacterium strains was assessed by cloning and examining the expression of an alpha-l-arabinofuranosidase gene belonging to Bifidobacterium longum. E. coli and Bifidobacterium pseudocatenulatum recombinant clones were stable and showed an increase in alpha-arabinofuranosidase activity of over 100-fold compared to that of the untransformed hosts.
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Abstract
The 2.1-kb cryptic plasmid pCIBAO89 from Bifidobacterium asteroides harbors a 1.4-kb segment which is sufficient for its autonomous replication. The segment is divided into two parts, the presumed replication origin, ori89, and the rep gene encoding the putative 41-kDa Rep89 replication initiation protein. This minimal replication region of pCIBAO89 was functionally dissected by transcriptional analyses as well as by DNA-binding studies, and the information obtained was exploited to create a number of Escherichia coli-Bifidobacterium shuttle vectors capable of transforming various bifidobacteria with an efficiency of up to 10(6) transformants/mug DNA.
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Alvarez-Martín P, O'Connell-Motherway M, van Sinderen D, Mayo B. Functional analysis of the pBC1 replicon from Bifidobacterium catenulatum L48. Appl Microbiol Biotechnol 2007; 76:1395-402. [PMID: 17704917 DOI: 10.1007/s00253-007-1115-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Revised: 07/06/2007] [Accepted: 07/07/2007] [Indexed: 10/22/2022]
Abstract
To determine the minimal replicon of pBC1 (a 2.5-kb cryptic plasmid of Bifidobacterium catenulatum L48) and to check the functionality of its identified open reading frames (ORFs) and surrounding sequences, different segments of pBC1 were amplified by polymerase chain reaction (PCR) and cloned into pBif, a replication probe vector for bifidobacteria. The largest fragment tested in this manner encompassed most of the pBC1 sequence, while the shortest just included the repB gene and its immediate upstream sequences. Derivatives were all shown to allow replication in bifidobacteria. Surprisingly, both the transformation frequency and segregational stability in the absence of antibiotic selection decreased with reducing plasmid length. The relative copy number of the constructs (ranging from around 3 to 23 copies per chromosome equivalent, as compared to 30 copies for the original pBC1) was shown to be strain dependent and to decrease with reducing plasmid length. These results suggest that, although not essential, the copG-like and orfX-like genes of pBC1 play important roles in pBC1 replication. Interruption of repB produced a construct incapable of replicating in bifidobacteria. The analysis of pBC1 will allow its use in the construction of general and specific cloning vectors.
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Affiliation(s)
- Pablo Alvarez-Martín
- Departamento de Microbiología y Bioquímica de Productos Lácteos, Instituto de Productos Lácteos de Asturias (CSIC), Carretera de Infiesto s/n, 33300 Villaviciosa, Asturias, Spain
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