Abstract
Among sequenced genomes, it is common to find a high proportion of genes encoding proteins that cannot be assigned a known function. In bacterial genomes, genes related to a similar function are often located in contiguous regions. The presence of genes encoding conserved hypothetical proteins (chp) in such a region may suggest that they are related to that particular function. Plasmid pRet42a from Rhizobium etli CFN42 is a conjugative plasmid containing a segment of approximately 30 Kb encoding genes involved in conjugative transfer. In addition to genes responsible for Dtr (DNA transfer and replication), Mpf (Mating pair formation) and regulation, it has two chp-encoding genes (RHE_PA00163 and RHE_PA00164) and a transcriptional regulator (RHE_PA00165). RHE_PA00163 encodes an uncharacterized protein conserved in bacteria that presents a COG4634 conserved domain, and RHE_PA00164 encodes an uncharacterized conserved protein with a DUF433 domain of unknown function. RHE_PA00165 presents a HTH_XRE domain, characteristic of DNA-binding proteins belonging to the xenobiotic response element family of transcriptional regulators. Interestingly, genes similar to these are also present in transfer regions of plasmids from other bacteria. To determine if these genes participate in conjugative transfer, we mutagenized them and analyzed their conjugative phenotype. A mutant in RHE_PA00163 showed a slight (10 times) but reproducible increase in transfer frequency from Rhizobium donors, while mutants in RHE_PA00164 and RHE_PA00165 lost their ability to transfer the plasmid from some Agrobacterium donors. Our results indicate that the chp-encoding genes located among conjugation genes are indeed related to this function. However, the participation of RHE_PA00164 and RHE_PA00165 is only revealed under very specific circumstances, and is not perceived when the plasmid is transferred from the original host. RHE_PA00163 seems to be a fine-tuning modulator for conjugative transfer.
Highlights
The availability of sequenced genomes has increased exponentially in the last years
We studied the participation of the chp- encoding genes localized in the transfer region, in the conjugative transfer (CT) ability of plasmid pRet42a of Rhizobium etli strain CFN42
Rhizobial plasmids have been classified in four groups; among them pRet42a belongs to group I, and pRet42d to group II
Summary
There are 168 complete sequences of archaea, 2788 of bacteria, and 222 of eukarya, according to NCBI. Analyses of the sequences usually show the presence of genes similar to others with known functions, but, invariably, genes with unknown function are present. Bacteria belonging to the rhizobia are able to form nitrogenfixing symbiosis with the roots of leguminous plants (MassonBoivin et al, 2009). The genomes of these bacteria are usually composed of a chromosome and various plasmids of sizes ranging between 150 and 1800 Kb. The plasmids may carry up to 40% of the total genomic content, including the information allowing the establishment of the symbiosis (Romero and Brom, 2004). The elements required for CT are a set of genes involved in the processing of DNA (Dtr, DNA transfer and replication), a set of genes involved in formation of the mating pair www.frontiersin.org
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
