Diversity and Evolution of Hydrogenase Systems in Rhizobia

Abstract

Uptake hydrogenases allow rhizobia to recycle the hydrogen generated in the nitrogen fixation process within the legume nodule. Hydrogenase (hup) systems in Bradyrhizobium japonicum and Rhizobium leguminosarum bv. viciae show highly conserved sequence and gene organization, but important differences exist in regulation and in the presence of specific genes. We have undertaken the characterization of hup gene clusters from Bradyrhizobium sp. (Lupinus), Bradyrhizobium sp. (Vigna), and Rhizobium tropici and Azorhizobium caulinodans strains with the aim of defining the extent of diversity in hup gene composition and regulation in endosymbiotic bacteria. Genomic DNA hybridizations using hupS, hupE, hupUV, hypB, and hoxA probes showed a diversity of intraspecific hup profiles within Bradyrhizobium sp. A large amount of hydrogen is released from legume root nodules during the nitrogen fixation process. This hydrogen production has been described as one of the major factors that affect the efficiency of symbiotic nitrogen fixation (39). Uptake hydrogenases allow endosymbiotic bacteria to oxidize the hydrogen produced by nitrogenase. This symbiotic hydrogen oxidation has been shown to reduce the energy losses associated with nitrogen fixation and to enhance productivity in certain legume hosts (1,14).A detailed characterization of the hydrogen uptake (hup) system has been carried out in Bradyrhizobium japonicum and Rhizobium leguminosarum bv. viciae (for a review, see reference 35). In both genera, the first component of this system is a membrane-bound, dimeric [NiFe] hydrogenase composed by two polypeptides of 35 and 65 kDa. These polypeptides are synthesized as precursors, which are proteolytically processed after metal cluster insertion. The hup genetic determinants are clustered in large DNA regions (20, 21), whose sequence analysis has revealed the presence of at least 17 common genes (hupSLCDFGHIJKhypABFCDEX) arranged in at least three operons with conserved gene composition and organization (35). Hydrogenase structural subunits are encoded by the hupS and hupL genes, whereas the remaining hup and hyp gene products are involved in the recruitment and incorporation of nickel and other metallic groups into the hydrogenase active site (for reviews, see references 12 and 35). Although the R. leguminosarum and B. japonicum hydrogenase systems are highly homologous, they show important differences in regulation and in the presence of specific genes. The hupE gene is specific for the R. leguminosarum UPM791 hup gene cluster. The function of its predicted product is unknown, but it has been proposed that it might act as a nickel transporter (35). In contrast, this strain lacks the hupNOP genes, whose gene products are involved in nickel metabolism in B. japonicum (16). Two completely different regulatory circuits control hydrogenase gene expression in these bacteria (36). Bradyrhizobium japonicum expresses hup genes in symbiosis as well as in microaerobic free-living cells. Four proteins are involved in regulation in this ...

Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains

“…While the BTAi1 hupS and hupL had 67% and 57% AA sequence identity to the same genes in T. denitrificans, they only had only 54% and 45% AA identity to orthologues of the same genes in the 'typical' chromosomal-borne hydrogenase gene cluster in strain BTAi1. In addition, both the pBTAi1 and T. denitrificans hydrogenase clusters each lacked hupC, hupG, and hupI and hupJ, which are typically found in the hydrogenase gene clusters in other rhizobia (Baginsky et al, 2002). Despite this similarity, the pBTAi1 hydrogenase gene cluster did not contain the isp1 and isp2 genes that separate the large and small hydrogenase genes in the T. denitrificans (Figure 3).…”

“…(Vigna) strains may have been acquired via horizontal transfer from a non-rhizobial source (Baginsky et al, 2002).…”

“…Generally, the hydrogen uptake (hup) genes are arranged in at least three operons with conserved gene composition and organization (Baginsky et al, 2002). The hupS and hupL genes encode for hydrogenase structural subunits, whereas the remaining hup and hyp gene products encode for maturation proteins, which are responsible for the recruitment and incorporation of nickel and other metals into the hydrogenase active site (Casalot and Rousset, 2001).…”

“…(Lupinus) and Bradyrhizobium sp. (Vigna), the hup genes have been presumed to be on the chromosome, since no plasmids could be detected in the strains examined by using standard plasmid isolation procedure (Baginsky et al, 2002;Brito et al, 2005).…”

Genomics of Specificity in the Symbiotic Interaction between Rhizobium leguminosarum and Legumes

“…R. leguminosarum bv. viciae UPM791, also a typical pea isolate, has been thoroughly used as inoculant (Nitragin strain 128C53, ) and studied for years by our group in view of its hydrogen recycling capabilities (Leyva et al, 1987, Brito et al, 1994, Gutierrez et al, 1997, Baginsky et al, 2002, Albareda et al, 2012.Other rhizobial strains were isolated from P1 soil, either from nodules, using plant hosts as traps (Tables M.2 and M.4), or directly from the soil (Table M.3). …”