BacA is indispensable for successful <Emphasis Type="Italic">Mesorhizobium</Emphasis>–<Emphasis Type="Italic">Astragalus</Emphasis> symbiosis

A homologue of Sinorhizobium meliloti bacA was isolated from Mesorhizobium huakuii 7653R, which is capable of fixing atmospheric nitrogen in symbiotic association with leguminous Astragalus sinicus (Chinese milk vetch). Inactivation of the bacA gene abolished the ability of M. huakuii 7653R to establish a successful symbiosis with its host plant. Simultaneously, compared with wild-type M. huakuii 7653R, the bacA mutant was more sensitive to cell envelope-disrupting agents (acidic solution, ethanol, SDS, and crystal violet). Mass spectrometry analysis revealed that the very-long-chain fatty acid (27-OHC-28:0 and 29-OHC-30:0) contents of lipid A was reduced in the M. huakuii 7653R bacA mutant. Taken together, our data suggest that the cell envelope was altered in the M. huakuii 7653R bacA mutant, which might deteriorate bacterial adaption to acute environmental changes encountered in host cells and ultimately result in the failure of Mesorhizobium–legume symbiosis. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification of a novel gene for biosynthesis of a bacteroid-specific electron carrier menaquinone

Ubiquinone (UQ) has been considered as an electron mediator in electron transfer that generates ATP in Rhizobium under both free-living and symbiosis conditions. When mutated, the dmtH gene has a symbiotic phenotype of forming ineffective nodules on Astragalus sinicus. The gene was isolated from a Mesorhizobium huakuii 7653R transposon-inserted mutant library. The DNA sequence and conserved protein domain analyses revealed that dmtH encodes demethylmenaquinone (DMK) methyltransferase, which catalyzes the terminal step of menaquinone (MK) biosynthesis. Comparative analysis indicated that dmtH homologs were present in only a few Rhizobia. Real-time quantitative PCR showed dmtH is a bacteroid-specific gene. The highest expression was seen at 25 days after inoculation of strain 7653R. Gene disruption and complementation tests demonstrated that the dmtH gene was essential for bacteroid development and symbiotic nitrogen fixation ability. MK and UQ were extracted from the wild type strain 7653R and mutant strain HK116. MK-7 was accumulated under microaerobic condition and UQ-10 was accumulated under aerobic condition in M. huakuii 7653R. The predicted function of DmtH protein was confirmed by the measurement of methyltransferase activity in vitro. These results revealed that MK-7 was used as an electron carrier instead of UQ in M. huakuii 7653R bacteroids.     

The NifA-RpoN Regulon of Mesorhizobium loti Strain R7A and Its Symbiotic Activation by a Novel LacI/GalR-Family Regulator

Mesorhizobium loti is the microsymbiont of Lotus species, including the model legume L. japonicus. M. loti differs from other rhizobia in that it contains two copies of the key nitrogen fixation regulatory gene nifA, nifA1 and nifA2, both of which are located on the symbiosis island ICEMlSym^R7A. M. loti R7A also contains two rpoN genes, rpoN1 located on the chromosome outside of ICEMlSym^R7A and rpoN2 that is located on ICEMlSym^R7A. The aims of the current work were to establish how nifA expression was activated in M. loti and to characterise the NifA-RpoN regulon. The nifA2 and rpoN2 genes were essential for nitrogen fixation whereas nifA1 and rpoN1 were dispensable. Expression of nifA2 was activated, possibly in response to an inositol derivative, by a novel regulator of the LacI/GalR family encoded by the fixV gene located upstream of nifA2. Other than the well-characterized nif/fix genes, most NifA2-regulated genes were not required for nitrogen fixation although they were strongly expressed in nodules. The NifA-regulated nifZ and fixU genes, along with nifQ which was not NifA-regulated, were required in M. loti for a fully effective symbiosis although they are not present in some other rhizobia. The NifA-regulated gene msi158 that encodes a porin was also required for a fully effective symbiosis. Several metabolic genes that lacked NifA-regulated promoters were strongly expressed in nodules in a NifA2-dependent manner but again mutants did not have an overt symbiotic phenotype. In summary, many genes encoded on ICEMlSym^R7A were strongly expressed in nodules but not free-living rhizobia, but were not essential for symbiotic nitrogen fixation. It seems likely that some of these genes have functional homologues elsewhere in the genome and that bacteroid metabolism may be sufficiently plastic to adapt to loss of certain enzymatic functions.     

Incompatibility behavior of a megaplasmid pMhHN3015c in Mesorhizobium huakuii HN3015

The Tn5-sacB-labeled symbiotic megaplasmid pMhHN3015c of Mesorhizobium huakuii HN3015 was, respectively, transferred into M. huakuii HN308SR containing three large plasmids of pMhHN308a, pMhHN308b and pMhHN308c, and 7653R-1SR, a symbiotic plasmid pMh7653Rb deleted mutant from M. huakuii 7653R by tri-parent mating. The stable indigenous plasmid pMhHN308c of HN308SR was cured by the introduction of pMhHN3015c and the transconjugant was named as HN308SRN18. The results implied that pMhHN3015c and pMhHN308c were incompatible and might be ascribed to the same incompatibility group. Furthermore, the results from plasmid curing tests of HN308SRN18 containing pMhHN3015c, pMhHN308b, and pMhHN308a showed that not only was pMhHN3015c deleted, but that pMhHN308a was also cured simultaneously. The plasmid profiles of transconjugant 7653R-1SRN18 showed pMhHN3015c could coexist with pMh7563Ra. The plasmid replication repC-like gene sequences were detected by polymerase chain reaction from 7653R-1SRN18, HN308SRN18 and its plasmid-curing derivatives, but failed to detect from plasmid-curing derivatives of 7653R-1SRN18. The repC gene sequence similarities of strains tested were up to 99%. Results from plant nodulation tests showed that introduction of pMhHN3015c failed to restore the nitrogen fixation ability of HN308SRN18 and 7653R-1SRN18.     

Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics

Background

Evidence based on genomic sequences is urgently needed to confirm the phylogenetic relationship between Mesorhizobium strain MAFF303099 and M. huakuii. To define underlying causes for the rather striking difference in host specificity between M. huakuii strain 7653R and MAFF303099, several probable determinants also require comparison at the genomic level. An improved understanding of mobile genetic elements that can be integrated into the main chromosomes of Mesorhizobium to form genomic islands would enrich our knowledge of how genome dynamics may contribute to Mesorhizobium evolution in general.

Results

In this study, we sequenced the complete genome of 7653R and compared it with five other Mesorhizobium genomes. Genomes of 7653R and MAFF303099 were found to share a large set of orthologs and, most importantly, a conserved chromosomal backbone and even larger perfectly conserved synteny blocks. We also identified candidate molecular differences responsible for the different host specificities of these two strains. Finally, we reconstructed an ancestral Mesorhizobium genomic island that has evolved into diverse forms in different Mesorhizobium species.

Conclusions

Our ortholog and synteny analyses firmly establish MAFF303099 as a strain of M. huakuii. Differences in nodulation factors and secretion systems T3SS, T4SS, and T6SS may be responsible for the unique host specificities of 7653R and MAFF303099 strains. The plasmids of 7653R may have arisen by excision of the original genomic island from the 7653R chromosome.

Electronic supplementary material

The online version of this article (doi: 10.1186/1471-2164-15-440) contains supplementary material, which is available to authorized users.     

华癸中慢生根瘤菌7653R 3个脂质转运蛋白基因的克隆、突变及共生表型北大核心CSCD

【目的】脂类转移家族蛋白基因编码一类参与脂类转运及代谢的蛋白。本研究旨在构建华癸中慢生根瘤菌3个脂质转运家族蛋白基因的突变株,检测及分析突变体与紫云英共生条件下的表型及功能。【方法】利用生物信息学分析与预测转脂蛋白的结构特征及功能,采用荧光定量技术检测目标基因在自生和共生条件下的表达特性,通过插入突变技术构建目标基因突变株,并进行植物盆栽实验考察其共生表型。【结果】MCHK-5577、MCHK-2172和MCHK-2779基因编码蛋白属于START/RHO alpha_C/PITP/Bet_v1/Cox G/Cal C(SRPBCC)超家族,包含脂类转移结构域,参与脂类转运或代谢,与百脉根等中慢生根瘤菌相应基因的序列相似性达95%以上。这3个基因在共生条件下的表达水平都增高。分别构建了MCHK-5577、MCHK-2172和MCHK-2779基因突变菌株,与野生型菌株7653R相比,接种突变株MCHK-2172mut、MCHK-2779mut和MCHK-5577mut后的植株地上部分生物量和根瘤固氮酶活性显著降低。【结论】华癸中慢生根瘤菌脂质转移家族蛋白基因在共生互作过程中发挥重要作用,突变后明显影响共生固氮表型。本文的实验结果为深入研究脂类转移蛋白在共生固氮作用中的功能机制奠定了基础。     

豌豆根瘤菌共生基因pJB5JI与华癸中生根瘤菌7653R共生质粒的相互关系

华癸中生根瘤菌(Mesorhizobium huakuii)7653R是分离自我国南方水稻田的一株根瘤菌,含有2个内源质粒:p7653Ra和p7653Rb,其中7653Rb是共生质粒.通过Tn5-sacB的插入方法来消除质粒,获得7653Rb消除的突变株7653RD.将豌豆根瘤菌T83K3的共生质粒pJB5JI导入7653R和7653RD中,盆栽结果表明含有pJB5JI的转移接合子7653R-197的竞争结瘤能力和共生固氮能力均高于7653R.pJB5JI不能恢复7653RD在紫云英上的结瘤能力.含有pJB5JI的7653RD可以在豌豆上结无效瘤,表明pJB5JI可以在7653R的染色体背景下表达其功能.对转移接合子中的质粒稳定性进行检测,结果表明pJB5JI在人工传代的情况下可以稳定存在,但经过共生之后发生了遗传分离,对转移接合子和出发菌株及分离菌株进行kan基因的PCR扩增,除了受体菌外其他菌株都可得到PCR产物,由此推测,pJB5JI可能部分或全部整合到了受体菌的染色体基因组中.     

Regulatory role of Rhizobium etli CNPAF512 fnrN during symbiosis

The Rhizobium etli CNPAF512 fnrN gene was identified in the fixABCX rpoN(2) region. The corresponding protein contains the hallmark residues characteristic of proteins belonging to the class IB group of Fnr-related proteins. The expression of R. etli fnrN is highly induced under free-living microaerobic conditions and during symbiosis. This microaerobic and symbiotic induction of fnrN is not controlled by the sigma factor RpoN and the symbiotic regulator nifA or fixLJ, but it is due to positive autoregulation. Inoculation of Phaseolus vulgaris with an R. etli fnrN mutant strain resulted in a severe reduction in the bacteroid nitrogen fixation capacity compared to the wild-type capacity, confirming the importance of FnrN during symbiosis. The expression of the R. etli fixN, fixG, and arcA genes is strictly controlled by fnrN under free-living microaerobic conditions and in bacteroids during symbiosis with the host. However, there is an additional level of regulation of fixN and fixG under symbiotic conditions. A phylogenetic analysis of the available rhizobial FnrN and FixK proteins grouped the proteins in three different clusters.     

Incompatibility behavior of a symbiotic plasmid pMH7653Rb in <Emphasis Type="Italic">Mesorhizobium huakuii</Emphasis> 7653R

Mesorhizobium huakuii strain 7653R harbored two indigenous plasmids named pMH7653Ra and pMH7653Rb. The larger plasmid pMH7653Rb (symbiotic plasmid) was transferred to M. huakuii HN308SR harboring three plasmids: pMHHN308a, pMHHN308b and pMHHN308c, and HN3015SR harboring three plasmids: pMHHN3015a, pMHHN3015b and pMHHN3015c by tri-parent mating. Two stable indigenous plasmids, pMHHN308b and pMHHN308c of HN308SR, were co-eliminated due to the introduction of pMH7653Rb, and the transconjugant was named HN308SRN14. The results implied that pMH7653Rb and pMHHN308b, pMHHN308c were incompatible and might have been ascribed to the same incompatible group. The plasmid profiles of transconjugant HN3015SRN14 showed that the second largest plasmid pMHHN3015b of HN3015SR was cured due to the introduction of pMH7653Rb. The results also implied that pMH7653Rb and pMHHN3015b were incompatible. Results from plant nodulation tests showed that pMH7653Rb could only maintain the nodulation ability in transconjugant HN308SRN14 and its nodule number was more than that of wild strain HN308SR, but could not replace the nitrogen fixation effect of pMHHN308b and pMHHN308c. The plasmid cured mutant HN308SRN14D harboring only pMHHN308a formed null nodules that demonstrated pMHHN308a was relevant to nodulation ability. HN3015SRN14 harboring pMH7653Rb, pMHHN3015a and pMHHN3015c formed null nodules while HN3015SRN14D containing pMHHN3015a and pMHHN3015c lost the nodulation ability. The plasmid replication repC-like gene sequences were detected by a polymerase chain reaction from 7653R, HN308, HN3015, HN308SRN14 and HN3015SRN14. The repC gene sequence similarities of the strains tested attained 99%.     

华癸根瘤菌外膜孔蛋白编码基因MCHK_1326突变株的构建与共生固氮表型分析

[目的]Mesorh izob ium huakuii 7653R的MCHK _1326基因编码一种外膜孔蛋白,可能参与根瘤菌侵染宿主植物以及结瘤固氮过程,本研究旨在探索该基因在共生固氮中的功能.[方法]生物信息学分析MCHK _1326蛋白的结构特征及生物学功能,启动子原位表达技术检测MCHK_1326共生时空表达特...     

Identification and Symbiotic Phenotype Characterization of an OPDA Reductase Gene <Emphasis Type="Italic">AsOPR1</Emphasis> in Chinese Milk Vetch

In higher plants, the 12-oxo-phytodienoic acid reductase (OPR) family mainly consists of two subgroups. OPR3-like enzymes belong to subgroup II, and they were proved to be key functional enzymes participating in jasmonic acid (JA) biosynthesis, while functions of OPR1-like enzymes classified into subgroup I remain largely unclear, particularly in symbiosis. This study identified and functionally characterized a gene encoding 12-oxophytodienoate reductase in Astragalus sinicus. Sequence homology analysis indicated that this gene encodes an OPR1-like enzyme. It was found that the gene expression of AsOPR1 was upregulated after inoculation with Mesorhizobium huakuii 7653R. Subcellular localization showed that in uninfected host plant cells, AsOPR1 was localized in the amyloplast, a differentiated form of plastid; while in the infected cells, AsOPR1 co-localized with rhizobia. Knockdown of the AsOPR1 gene decreased the nodule number to 34.6% that of the control roots, and significantly reduced the JA level in both transgenic roots and nodules, while overexpression of the AsOPR1 gene resulted in enlarged nodule meristem, but caused no changes in nodule number. Taken together, these results indicate that AsOPR1 may participate in the regulation of nodule formation and development, as well as affect endogenous JA metabolism.     

Characteristics of Plasmids in Rhizobium huakuii

Rhizobium huakuii nodulates Astragalus sinicus, an important green manuring crop in Southern China, which can be used as forage. The plasmid profiles of 154 R. huakuii strains were examined with the Eckhardt procedure. The plasmid number of the strains varied from one to five, and their molecular weights were estimated from 42 to 600 mDa or more. The plasmids were hybridized with probes nodABC and nifHDK. The results showed that there was one plasmid carrying the nod and nif genes in the strains that harbor two or more plasmids, and the molecular weights of the symbiotic plasmids varied from 117 to 251 mDa. Homology was not observed on plasmids in the strains having only one plasmid; presumably the symbiotic genes are on the chromosome. Plasmid curing was carried out with the Bacillus subtilus sacB to generate derivatives of Rhizobium huakuii strain CH203, which harbors three plasmids, pRHa(97MD), pRHb(168MD), and pRHc(251MD). The largest plasmid (pRHc) carried both nodulation and nitrogen fixation genes. When pRHc was cured, the strain lost its symbiotic ability. The other two plasmids were also related to symbiosis. The derivative cured of pRHb did not nodulate on the host plant, had an altered lipopolysaccharide, and grew much more slowly than the parent strain. Curing of the smallest plasmid (pRHa) resulted in delaying the strain nodulation and made it lose nitrogen fixation ability. Curing of each plasmid in strain CH203 reduced its acid tolerance. Complementation of plasmid-cured strains with appropriate plasmids restored their original phenotypes. Received: 18 December 1996 / Accepted: 28 March 1997     

Behavior of plasmid pJB5JI in Rhizobium huakuii under free-living and symbiotic conditions

The Rhizobium leguminosarum biovar viceae host-range plasmid pJB5JI was transferred into Rhizobium huakuii strains, both wild-type 7653R and its sym plasmid-cured mutant 7653R-1. Transconjugant 7653R-1 (pJB5JI) acquired the ability to form ineffective nodules on pea plants, whereas transconjugant 7653R (pJB5JI) could not do so, indicating that the indigenous symbiotic plasmid could restrict the functional expression of pJB5JI. On the other hand, transconjugant 7653R (pJB5JI) showed higher nitrogenase activity on A. sinicus and higher shoot dry weight than the recipient strain 7653R. The alien plasmid pJB5JI in both kinds of transconjugants remained stable during frequent transfer on culture media, but in part of the isolates from nodules formed by them the pJB5JI was not visualized on gel by the Eckhardt procedure. Southern hybridization with Tn5 and nod gene probes showed that these isolates still reserved, at least in part, DNA of pJB5JI, which was probably intergrated onto the chromosome of cells.     

Stable Isotope Probing with 15N2 Reveals Novel Noncultivated Diazotrophs in Soil

Biological nitrogen fixation is a fundamental component of the nitrogen cycle and is the dominant natural process through which fixed nitrogen is made available to the biosphere. While the process of nitrogen fixation has been studied extensively with a limited set of cultivated isolates, examinations of nifH gene diversity in natural systems reveal the existence of a wide range of noncultivated diazotrophs. These noncultivated diazotrophs remain uncharacterized, as do their contributions to nitrogen fixation in natural systems. We have employed a novel ¹⁵N₂-DNA stable isotope probing (⁵N₂-DNA-SIP) method to identify free-living diazotrophs in soil that are responsible for nitrogen fixation in situ. Analyses of 16S rRNA genes from ¹⁵N-labeled DNA provide evidence for nitrogen fixation by three microbial groups, one of which belongs to the Rhizobiales while the other two represent deeply divergent lineages of noncultivated bacteria within the Betaproteobacteria and Actinobacteria, respectively. Analysis of nifH genes from ¹⁵N-labeled DNA also revealed three microbial groups, one of which was associated with Alphaproteobacteria while the others were associated with two noncultivated groups that are deeply divergent within nifH cluster I. These results reveal that noncultivated free-living diazotrophs can mediate nitrogen fixation in soils and that ¹⁵N₂-DNA-SIP can be used to gain access to DNA from these organisms. In addition, this research provides the first evidence for nitrogen fixation by Actinobacteria outside of the order Actinomycetales.     

Relation between Glutamine Synthetase and Nitrogenase Activities in the Symbiotic Association between Rhizobium japonicum and Glycine max

The activity and extent of adenylylation of glutamine synthetase was examined in both free-living and bacteroid forms of Rhizobium japonicum in the presence of excess ammonia. Ammonia caused an apparent repression of glutamine synthetase in free-living R. japonicum and adenylylation of the enzyme was also increased. In contrast, neither the activity nor the extent of adenylylation of the bacteroid enzyme was consistently affected by ammonium treatment of bacteroid suspensions. Similar results were obtained after ammonium treatment of soybean plants even though nitrogenase activity was reduced markedly. We have been unable to demonstrate ammonium repression of nitrogenase activity in R. japonicum-Glycine max symbiotic association that is mediated through bacteroid glutamine synthetase. This result is in contrast to the situation in nitrogen-fixing strains of Klebsiella where a role of glutamine synthetase in the regulation of nitrogenase has been reported.