Analysis of the sequence of a new cryptic plasmid, pRJF2, from a rumen bacterium of the genus Butyrivibrio: comparison with other Butyrivibrio plasmids and application in the development of cloning vector

The large episomes of Butyrivibrio proteoclasticus B316T have arisen through intragenomic gene shuttling from the chromosome to smaller Butyrivibrio-specific plasmids

The genome of Butyrivibrio proteoclasticus B316(T) contains three large episomes including a 302 kb chromid (BPc2) and two large plasmids of 361 (pCY360) and 186 kb (pCY186). The two plasmids are largely cryptic and it is therefore difficult to gauge their contributions or importance to the biology of B. proteoclasticus. Here, we provide evidence that at least BPc2 and pCY360 are essential as neither could be cured using several previously described curing techniques. We show that BPc2 exists at a copy number of 1, while pCY360 and pCY186 exist at copy numbers of 4 and 0.9, respectively. Yet the transcriptional activities of each episome are much less than that of the 3.5 Mb chromosome. Codon usage analyses did not support the hypothesis that the genes of all three episomes were acquired horizontally. Instead our analyses suggest that the vast majority of genes on each episome were transferred from the 3.5 Mb B. proteoclasticus chromosome. Analysis of their replication origins, however, suggests the plasmid backbones share an evolutionary lineage with the smaller Butyrivibrio specific plasmids, pRJF1 and pRJF2. A survey of 13 species of the Butyrivibrio/Pseudobutyrivibrio assemblage identified similar large episomes in nine strains. DNA hybridization experiments revealed none contained an rRNA operon and only a 145 kb episome from Pseudobutyrivibrioruminis possessed an ortholog of the pCY360 plasmid replication initiation protein. The size and distribution of episomes within the nine strains of Butyrivibrio/Pseudobutyrivibrio showed no correlation with 16S rRNA based phylogeny, leading to a hypothesis that the large episomes of Butyrivibrio spp., have arisen through intragenomic gene transfer events from the chromosome to small horizontally acquired elements.

pSRD191, a new member of RepL replicating plasmid family from Selenomonas ruminantium

A numerous plasmid population was detected in strain 19 of Selenomonas ruminantium. The population was found to consist of six plasmids in size ranging from 1.4 to more than 20kb. The smallest 1.4kb cryptic plasmid pSRD191 was further characterized. Sequence analysis identified a single ORF encoding the 177-residue putative replication protein (Rep191) which shared significant homology with RepL family of replication protein from Firmicutes (staphylococci and bacilli). PCR analysis and Southern hybridisation showed that pSRD191 related plasmids are frequently encountered in rumen selenomonads.

Expression and export of aRuminococcus albuscellulase inButyrivibrio fibrisolvensthrough the use of an alternative gene promoter and signal sequence

Ruminococcal cellulase (Ruminococcus albus F-40 endoglucanase EgI) was successfully expressed in Butyrivibrio fibrisolvens OB156C, using the erm promoter from pAMβ1. A newly identified signal peptide coding region of xynA from B. fibrisolvens 49 allowed efficient translocation of the foreign EgI into the extracellular fraction. First, B. fibrisolvens xynA with or without its own putative signal peptide (XynA SP) coding region was cloned into a shuttle vector to transform B. fibrisolvens OB156C. Both plasmids caused a 2- to 2.4-fold increase in xylanase activity. The transformant expressing XynA with the signal peptide showed a significantly higher proportion of activity in the extracellular fraction than the transformant with XynA lacking the signal peptide (75% vs. 19%), demonstrating the significance of XynA SP in the translocation of the expressed enzyme. Second, using the XynA SP coding region, secretion of EgI was attempted in B. fibrisolvens. Since the signal peptide of R. albus EgI did not function in B. fibrisolvens, it was replaced with the XynA SP. A high activity variant of EgI containing the XynA SP was transcribed using the erm promoter, resulting in a 27-fold increase in endoglucanase activity, most of which (>93%) was in the extracellular fraction of the B. fibrisolvens transformant. EgI without the XynA SP was scarcely detected in the extracellular fraction (<10%).Key words: Butyrivibrio fibrisolvens, Ruminococcus albus, cellulase, gene promoter, signal peptide.

Development and use of competitive PCR assays for the rumen cellulolytic bacteria: Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens

Competitive PCR assays were developed for the enumeration of the rumen cellulolytic bacterial species: Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens. The assays, targeting species-specific regions of 16S rDNA, were evaluated using DNA from pure culture and rumen digesta spiked with the relevant cellulolytic species. Minimum detection levels for F. succinogenes, R. albus and R. flavefaciens were 1-10 cells in pure culture and 10(3-4) cells per ml in mixed culture. The assays were reproducible and 11-13% inter- and intra-assay variations were observed. Enumeration of the cellulolytic species in the rumen and alimentary tract of sheep found F. succinogenes dominant (10(7) per ml of rumen digesta) compared to the Ruminococcus spp. (10(4-6) per ml). The population size of the three species did not change after the proportion of dietary alfalfa hay was increased. All three species were detected in the rumen, omasum, caecum, colon and rectum. Numbers of the cellulolytic species at these sites varied within and between animals.

Development of a competitive polymerase chain reaction assay for the ruminal bacterium Butyrivibrio fibrisolvens OB156 and its use for tracking an OB156-derived recombinant

A competitive polymerase chain reaction assay targeting the 16S rDNA was developed for quantitating the rumen bacterium Butyrivibrio fibrisolvens OB156. A competitor DNA, serving as an internal control in the competitive polymerase chain reaction reaction, was constructed by polymerase chain reaction using a looped oligo longer than the normal primer. Coamplification of the target DNA with known amounts of the competitor DNA allowed quantitation of the target DNA in both pure culture and mixed culture systems, where minimum quantifiable level of OB156 was 1.7x10(2) and 5.6x10(4) cells, respectively. When an erythromycin-resistant recombinant derived from OB156 was inoculated into a rumen fluid culture, its numbers decreased with time. The rate of decrease measured by the competitive polymerase chain reaction assay was much slower than the rate determined by culture enumeration using erythromycin selection. The competitive polymerase chain reaction assay also showed 48 h persistence of the recombinant at 10(4) ml(-1) even after disappearance of culturable recombinant, suggesting maintenance of the target DNA from uncultivable cells. In an in vivo tracking trial, the recombinant became undetectable within 72 h with either assay, indicating rapid hydrolysis and/or outflow of the cells from the rumen.

A small cryptic plasmid from Ruminobacter amylophilus NIAH-3 possesses functional mobilization properties

The complete nucleotide sequence of a small cryptic plasmid designated pRAO1, from the Gram-negative ruminal bacterium Ruminobacter amylophilus NIAH-3, was determined. The plasmid is a circular DNA molecule, 2140 bp in size, with a GC content of 40%. Computer-assisted analysis identified three open reading frames (ORFs), one of which, ORF3 (347 amino acids), displayed a high degree of amino acid identity with the Mob proteins involved in conjugative mobilization and interplasmid recombination of plasmids from Gram-positive bacteria. We proved the mobilization properties of pRAO1 in the Escherichia coli system using the coresident IncW broad-host-range conjugative plasmid R388. These data demonstrated, for the first time, the mobilization properties of small cryptic plasmids from Gram-negative inhabitants of the rumen.

Constitutive expression of a heterologous Eubacterium ruminantium xylanase gene (xynA) in Butyrivibrio fibrisolvens

An Eubacterium ruminantium xylanase gene (xynA) was inserted into pYK4, a shuttle vector replicable in both Escherichia coli and Butyrivibrio fibrisolvens, and the resultant chimeric plasmid (pYK4XT) was electroporated into B. fibrisolvens OB156C in an attempt to obtain a more xylanolytic B. fibrisolvens. Electrotransformants were screened by the development of erythromycin resistance, followed by an activity staining and Southern hybridization. The presence of mRNA from xynA in the transformant, B. fibrisolvens NO4, was confirmed by Northern hybridization. Xylanase activity of the transformant NO4 was apparently enhanced regardless of carbon sources in the medium. When grown on glucose or cellobiose. NO4 had approximately 5-6 times higher intracellular activity than the parent OB156C on a culture volume basis as well as protein basis. The transformant showed extracellular xylanase activity much higher (between 7- and 10(4)-fold) than the parent. Transformant NO4 recorded the highest activity when grown on xylan. Most (> 90%) of the activity was extracellular. The extracellular activity was 2-fold greater in NO4. These findings indicate that the introduced xynA was expressed constitutively and the xylanase protein was exported into the culture supernatant. Growth of NO4 on glucose was similar to that of OB156C, which suggests little extra load for plasmid maintenance and foreign xylanase production in the transformant. The plasmid pYK4XT was maintained stably in the transformant for more than 100 generations.

Structural analysis of a new cryptic plasmid pAR67 isolated from Ruminococcus albus AR67

The complete nucleotide sequence of a new cryptic plasmid pAR67 isolated from a rumen bacterium Ruminococcus albus AR67 has been determined. The plasmid pAR67 was 3419 bp in size with a 45% GC content. Two open reading frames, ORF1 and ORF2, encoding potential polypeptides of 285 and 165 amino acids, with limited sequence similarity to replication and mobilization proteins, respectively, were identified within the sequence. The region upstream of ORF1 had an AT-rich (80%) segment followed by four 19-bp direct repeats, which is similar to the structural organization characteristic of replication origins of some bacterial plasmids.

High-frequency transfer of a naturally occurring chromosomal tetracycline resistance element in the ruminal anaerobe Butyrivibrio fibrisolvens

Butyrivibrio fibrisolvens strains resistant to tetracycline were isolated from the bovine rumen. Two of three Tcr B. fibrisolvens tested were able to donate tetracycline resistance at frequencies ranging from 10(-7) to 10(-1) per donor cell in anaerobic filter matings to a rifampin-resistant mutant of the type strain of B.fibrisolvens, 2221R. The recipient strain 2221R exhibited rapid autoaggregation, which might be a factor in the high transfer rates observed. Tcr transconjugants of B. fibrisolvens 2221R were also capable of further transferring tetracycline resistance to a fusidic acid-resistant mutant, 2221F. Comparison of genomic DNAs by pulsed-field gel electrophoresis demonstrated altered band profiles in transconjugants, consistent with the acquisition of a large mobile chromosomal element. The transferable elements from the two B. fibrisolvens donors 1.23 and 1.230 (TnB123 and TnB1230, respectively) showed the same preferred insertion site in the B. fibrisolvens 2221R chromosome and are likely to be similar, or identical, elements. Hybridization experiments showed no close relationship between TnB1230 and int-xis regions from Tn916 or Tn5253. Although DNA from the B. fibrisolvens donor strains hybridized with probes carrying tet(M) or tet(O) sequences, transconjugants were found to have acquired a distinct band that hybridized only weakly with these probes, suggesting that a second, distantly related Tcr determinant had been transferred.

Sequence analysis and characterization of pOM1, a small cryptic plasmid from Butyrivibrio fibrisolvens, and its use in construction of a new family of cloning vectors for Butyrivibrios

As a preliminary step in the development of vector systems, we have isolated and begun to characterize small, cryptic plasmids from several strains of the rumen bacterium Butyrivibrio fibrisolvens. We present here the complete nucleotide sequence of Butyrivibrio plasmid pOM1, which was isolated from B. fibrisolvens Bu49. While it is very similar in size to the previously characterized Butyrivibrio plasmids pRJF1 and pRJF2, pOM1 exhibits a restriction pattern which is quite distinct. Analysis of sequence data reveals that pOM1 contains only two open reading frames of significant length (ORF1 and ORF2), both of which are required for self-replication and maintenance. The protein encoded in ORF1 shows homologies with Pre (plasmid recombination enzyme) proteins encoded in plasmids from gram-positive organisms such as Staphylococcus aureus, Streptococcus agalactiae, Lactobacillus plantarum, and Bacillus thuringiensis. The putative translation product of ORF2, on the other hand, resembles Rep (replication) proteins of a different group of gram-positive plasmids, for which the Staphylococcus plasmid pSN2 is a prototype. Unlike the other characterized-Butyrivibrio plasmids, pOM1 appears to replicate via a rolling-circle mechanism. Experimental evidence showing the presence of a single-stranded replication intermediate consistent with this mechanism is presented. pOM1 has been used in the construction of a new Escherichia coli-B. fibrisolvens shuttle vector, pSMerm1, which has been successfully used to introduce a cloned gene into B. fibrisolvens harboring the pRJF1 plasmid.

Group-specific 16S rRNA hybridization probes for determinative and community structure studies of Butyrivibrio fibrisolvens in the rumen

Oligonucleotide probes covering three phylogenetically defined groups of Butyrivibrio spp. were successfully designed and tested. The specificity of each probe was examined by hybridization to rRNAs from an assortment of B. fibrisolvens isolates as well as additional ruminal and nonruminal bacteria. The sensitivity of the hybridization method was determined by using one of the probes (probe 156). When RNA was extracted from a culture of OB156, the probe was able to detect target cells at densities as low as 10(4) cells/ml. When 10(4) or more target cells/ml were added to cattle rumen samples, detectable hybridization signals were obtained with 1,000 ng of total RNA loaded onto the nylon membrane. In contrast, the sensitivity was reduced to 10(6) target cells/ml at 100 ng of RNA per slot. The probes were used to type 19 novel Butyrivibrio isolates. The phylogenetic placement was confirmed by partial 16S rRNA gene sequencing. The use of the probes in community-based studies indicated that the Butyrivibrio groups examined in this paper did not represent a significant portion of the bacterial 16S rRNA pool in the rumen of the cattle, sheep, and deer examined.

Are ruminal bacteria armed with bacteriocins?

The production of toxic compounds or antibiotics is a common component of intermicrobial competitive interactions, and many of these toxins have been adopted and adapted for the control of microbial populations. One class of these toxins, the bacteriocins, is a heterogeneous group of proteinaceous antibiotics that often display a high degree of target specificity, although many have a very wide spectrum of activity. To date, only limited information is available concerning the occurrence of bacteriocins among ruminal isolates or the sensitivity of ruminal microorganisms to exogenous bacteriocins. A survey of 50 strains of Butyrivibrio spp. isolated from a variety of sources (sheep, deer, and cattle) for bacteriocin production indicated a high incidence of bacteriocin-like activity (50%). Many of these inhibitory compounds appear to have a broad spectrum of activity, which suggests that bacteriocins may have a significant impact on both the competitive fitness of individual microbial strains within the rumen and on the overall structure of the microbial population within the rumen. Selected bacteriocins from lactic acid bacteria also were shown to have activity against Butyrivibrio spp. and may have application in ruminant systems. Bacteriocins may provide an alternative group of antibiotics for the manipulation of ruminal microbial populations. Bacteriocins have significant advantages over other antibiotics in target specificity, susceptibility to proteolytic digestion, possibility of genetic transfer and manipulation, and, in the case of some bacteriocins derived from lactic acid bacteria, a long history of safe use.

Complete nucleotide sequence of a cryptic plasmid, pBAW301, from the ruminal anaerobe Ruminococcus flavefaciens R13e2

The complete nucleotide sequence of a cryptic plasmid designated pBAW301, from the Gram-positive ruminal bacterium Ruminococcus flavefaciens R13e2, has been determined. This plasmid is 1768 bp in size and has an overall G+C content of 43.5%. Computer analysis of the sequence data revealed an open reading frame, ORF1 (256 amino acids), which is similar to the Rep protein of the Bacillus borstelensis plasmid pHT926. ORF1 is preceded by Shine-Dalgarno and Escherichia coli-10 and -35 like sequences. Nine smaller open reading frames showed no significant homologies to known protein sequences. Analysis of replication intermediates and the nucleotide sequence indicate that the plasmid does not replicate by a rolling-circle mode of replication similar to other plasmids from Gram-positive bacteria. Moreover, sequences typical of theta replication origins were not found in the nucleotide sequence of pBAW301. These data suggest that this plasmid either replicates by an as yet undescribed mechanism, or represents a new class of theta replicating plasmids.

16S rDNA analysis of Butyrivibrio fibrisolvens: phylogenetic position and relation to butyrate-producing anaerobic bacteria from the rumen of white-tailed deer

Complete 16S rDNA sequences of six strains of Butyrivibrio fibrisolvens, including the type strain (ATCC 19171), were determined. The type strain was found to have less than 89% sequence similarity to the other isolates that were examined. The five plasmid-bearing strains formed a closely related cluster and three of these strains (OB156, OB157 and OB192) were very highly related (> 99%), indicating that they are isolates of the same genomic species. The phylogenetic position of Butyrivibrio was found to be within the subphylum Clostridium, of Gram-positive bacteria. The closest relatives to the type strain were Eubacterium cellulosolvens and Cl. xylanolyticum and the closest relatives to the separately clustered strains were Roseburia ceciola, Lachnospira pectinoschiza and Eubacterium rectale.