A newEscherichia coli: Bacteroides shuttle vector, pRRI207, based on theBacteroides ruminicola plasmid replicon pRRI2

Non-oral Prevotella stepping into the spotlight

Species now affiliated to genus Prevotella have been known for decades as an integral part of human oral cavity microbiota. They were frequently isolated from patients with periodontitis or from dental root canals but also from healthy subjects. With the exception of Prevotella intermedia, they were considered opportunistic pathogens, as they were isolated also from various bacterial abscesses from the head, neck, breast, skin and various other body sites. Consequently, Prevotella were not in the focus of research activities. On the other hand, the four species found in the rumen never caused any disease and seemed early on to be numerous and important part of the rumen ecosystem indicating this genus harbored bacteria with enormously diverse habitats and lifestyles. The purpose of this review is to illustrate the main research themes performed in Prevotella on a path from less noted oral bacteria and from hard to cultivate and study rumen organisms to important mutualistic bacteria in guts of various mammals warranting major research efforts.

Lightning-triggered electroporation and electrofusion as possible contributors to natural horizontal gene transfer

Phylogenetic studies show that horizontal gene transfer (HGT) is a significant contributor to genetic variability of prokaryotes, and was perhaps even more abundant during the early evolution. Hitherto, research of natural HGT has mainly focused on three mechanisms of DNA transfer: conjugation, natural competence, and viral transduction. This paper discusses the feasibility of a fourth such mechanism--cell electroporation and/or electrofusion triggered by atmospheric electrostatic discharges (lightnings). A description of electroporation as a phenomenon is followed by a review of experimental evidence that electroporation of prokaryotes in aqueous environments can result in release of non-denatured DNA, as well as uptake of DNA from the surroundings and transformation. Similarly, a description of electrofusion is followed by a review of experiments showing that prokaryotes devoid of cell wall can electrofuse into hybrids expressing the genes of their both precursors. Under sufficiently fine-tuned conditions, electroporation and electrofusion are efficient tools for artificial transformation and hybridization, respectively, but the quantitative analysis developed here shows that conditions for electroporation-based DNA release, DNA uptake and transformation, as well as for electrofusion are also present in many natural aqueous environments exposed to lightnings. Electroporation is thus a plausible contributor to natural HGT among prokaryotes, and could have been particularly important during the early evolution, when the other mechanisms might have been scarcer or nonexistent. In modern prokaryotes, natural absence of the cell wall is rare, but it is reasonable to assume that the wall has formed during a certain stage of evolution, and at least prior to this, electrofusion could also have contributed to natural HGT. The concluding section outlines several guidelines for assessment of the feasibility of lightning-triggered HGT.

Type II restriction modification systems of Prevotella bryantii TC1-1 and Prevotella ruminicola 23 strains and their effect on the efficiency of DNA introduction via electroporation

The restriction endonucleases PbrTI and Pru2I, isoschizomers of Sau3AI and HaeIII, were partially purified and characterized from anaerobic rumen bacteria Prevotella bryantii TC1-1 and Prevotella ruminicola 23, respectively. These are the first type II restriction endonucleases discovered in strains of the genus Prevotella, and they represent one of the barriers hindering gene transfer in these microorganisms. Heterologous DNA was protected against the action of the PbrTI or Pru2I by incubation in a cell-free extract of the respective strain which contained 20 mM EDTA. This led to the development of a protocol enabling successful electrotransformation of the P. bryantii TC1-1 strain with a pRH3 Bacteroides--Escherichia coli shuttle vector containing up to 7-kb long DNA inserts. Plasmid DNA isolated from the transformed strain facilitated the transfer with further increased efficiency and made possible the introduction of ligation reaction products directly to P. bryantii TC1-1 without passing them first through E. coli.

Sequence analysis of the plasmid pRRI2 from the rumen bacterium Prevotella ruminicola 223/M2/7 and the use of pRRI2 in Prevotella/Bacteroides Shuttle Vectors

pRRI2 is a small cryptic plasmid from the rumen bacterium Prevotella ruminicola 223/M2/7 which has been used for the construction of shuttle vectors (pRH3 and pRRI207) that replicate in many Bacteroides/Prevotella strains as well as in Escherichia coli. Sequence analysis of pRRI2 reveals that it is a 3240-bp plasmid carrying two clear open reading frames. Rep, encoded by ORF1, shows 48 and 47% amino acid sequence identity with RepA proteins from Bacteroides vulgatus and Bacteroides fragilis, respectively. ORF2, named Pre, shares 34% amino acid sequence identity with a putative plasmid recombination protein from the Flavobacterium spp. plasmid pFL1 and 30% amino acid sequence identity with BmpH from B. fragilis Tn5520. Disruption of ORF1 with HindIII prevents replication and maintenance in Bacteroides spp. hosts, but shuttle vectors carrying pRRI2 interrupted within ORF2, by EcoRI*, are able to replicate. pRRI2 shows no significant similarity with the only other P. ruminicola plasmid to have been studied previously, pRAM4.

Construction of Prevotella ruminicola-Escherichia coli shuttle vector pRAM45 and transformation of P. ruminicola strains by electroporation

A new plasmid shuttle vector, pRAM45, was constructed from the Escherichia coli plasmid pACYC184 and the cryptic plasmid pRAM4, which was originally isolated by us from Prevotella ruminicola T31 (Ogata et al., Plasmid, 35, 91-97, 1996). The vector was electrotransformed into different P. ruminicola strains. Polymerase chain reaction and Southern hybridization experiments confirmed its integrity in P. ruminicola transformants.

Engineering gut flora of ruminant livestock to reduce forage toxicity: progress and problems

The rumen bacterium Butyrivibrio fibrosolvens has been genetically modified to detoxify fluoroacetate (a poisonous component of trees and shrubs in Australia, Africa and Central America) and has been shown to persist when it is returned to the rumen. Such bacteria may save animals from poisoning and, therefore, reduce economic losses for livestock industries in those countries. The ability to make genetic changes to rumen bacteria raises important questions about their practicality, and about the environmental factors that must be considered before releasing modified strains. The fluoroacetate-detoxifying bacterium provides an important model by which these issues can be examined.

Expression of a cloned cellulase/xylanase gene from Prevotella ruminicola in Bacteroides vulgatus, Bacteroides uniformis and Prevotella ruminicola

A new shuttle vector, pRH3 (8.7 kb), was constructed for use in Prevotella/Bacteroides host strains. This vector combines the pRRI2 replicon from P. ruminicola, pBluescript sequences and a tetQ marker gene for selection in Prevotella/Bacteroides hosts. Following insertion of a fragment carrying an endoglucanase/xylanase gene from P. ruminicola 23 into the multiple cloning site, the resulting construct, pRH3X, was introduced into B. vulgatus 1447, B. uniformis 1100 and P. ruminicola 2202. This resulted in increases of between 4 and 50-fold in CM-cellulase and xylanase activities in cells grown with glucose. In contrast activities were barely detectable for the same construct in E. coli DH5 alpha. Most of the total xylanase activity produced was found within the cell in P. ruminicola 2202 and B. vulgatus 1447 transformed with pRH3X, and in P. ruminicola 23. An osmotic shock experiment indicated that a significant proportion of the xylanase activity in B. vulgatus 1447 cells carrying pRH3X was periplasmic.

Detoxification of the plant toxin fluoroacetate by a genetically modified rumen bacterium

We isolated the fluoroacetate dehalogenase gene (H1), from Moraxella species strain B, and placed it under the transcriptional control of a 154 bp fragment of the erm gene promoter. The promoter/gene construct was attached to the Butyrivibrio fibrisolvens shuttle vector pBHerm, and the resulting dehalogenase expression plasmid (pBHf) was transferred to B. fibrisolvens OB156 by electroporation. The erm gene promoter directed expression of dehalogenase activity in both E. coli and B. fibrisolvens OB156. Cell-free lysates of the genetically modified OB156 defluorinated 10.6 nmol fluoroacetate/min/mg protein. Growing cultures of OB156 were able to detoxify fluoroacetate in the culture medium, at the rate of 9.9 nmol/min/mg. Plasmid pBHf was retained by 100% of OB156 cells after 500 generations of non-selective culture. The restriction pattern of pBHf remained unchanged after extensive non-selective growth and host bacteria continued to produce active dehalogenase. The construction of rumen bacteria that are able to detoxify an important natural poison supports the feasibility of using genetically modified rumen bacteria to aid animal production.

Molecular genetics of obligate anaerobes from the rumen

The rumen is inhabited by a highly specialised microflora consisting of obligately anaerobic bacteria, fungi and protozoa. Rumen bacteria belong to many different phylogenetic groupings and many species exhibit a high degree of rRNA gene sequence diversity, whereas the rumen fungi are monophyletic. At least 21 genes concerned with the degradation and utilisation of plant cell wall polysaccharides, from five species of rumen bacteria and from rumen fungi, have been isolated and sequenced. In general, the catalytic domains of the encoded enzymes belong to enzyme families identified among non-rumen microorganisms, but some show unusual organisation, consisting of multiple catalytic domains. Several bacterial species have been used as recipients for gene transfer by electrotransformation or by conjugation, allowing development of methods for genetic analysis. The rumen is also considered as a potential site for natural gene transfer.

Molecular cloning and expression in Escherichia coli of genes encoding pectate lyase and pectin methylesterase activities from Bacteroides thetaiotaomicron

Bacteroides thetaiotaomicron strain 217 can use pectins as a sole carbon source. Preliminary characterization of the pectinolytic enzymes revealed three complementary activities in this strain: a pectin methylesterase (PME), a pectate lyase (PL) and a polygalacturonase (PG), which were all inducible by pectin or polygalacturonate. Use of the lambdoid phage replacement vector lambda EMBL3 allowed a 13.2 kb insert mediating both PL and PME activities to be isolated. Subcloning of two EcoRI fragments in pBR325 led to the separate isolation of the pel and pme genes. They were expressed constitutively in Escherichia coli HB101, as proved by the activities observed even in mineral medium supplemented only with glucose. In addition, the pme gene was expressed in both orientations. These results suggest that each gene represents an individual transcriptional unit. Several properties of the cloned PL were different from those of the original strain: it was mainly associated to the outer membrane, its optimum pH was higher, and its stability at 50 degrees C was lost but partially preserved by CaCl2. In addition, the apparent specific PL activity in the E. coli membrane fraction was about 30-fold higher. On the other hand, most of the properties of the cloned PME were similar to those of the original. Despite an enhanced thermostability, the apparent specific activity of the cloned PME was about 6-fold lower, and was independent of the insert orientation.

Complete nucleotide sequence of a Selenomonas ruminantium plasmid and definition of a region necessary for its replication in Escherichia coli

A plasmid from Selenomonas ruminantium subspecies lactilytica has been subcloned in Escherichia coli K-12 and completely sequenced. Three open reading frames (ORFs) of 909, 801, and 549 bp were identified and the complete sequence was analyzed by comparison with DNA and protein databases. No significant deoxynucleotide or amino acid sequence homology with other published genes or proteins was detected. The plasmid was shown to replicate independently in E. coli K-12 by a DNA polymerase I-dependent mechanism and deletion analysis defined the DNA sequence responsible for this phenotype.