Soybean nodulin genes: Analysis of cDNA clones reveals several major tissue-specific sequences in nitrogen-fixing root nodules

Identification of key genes involved in root development of tomato using expressed sequence tag analysis

Root system of plants are actually fascinating structures, not only critical for plant development, but also important for storage and conduction. Due to its agronomic importance, identification of genes involved in root development has been a subject of intense study. Tomato is the one of the most consumed vegetables in the world. Tomato has been used as model system for dicot plants because of its small genome, well-established transformation techniques and well-constructed physical map. The present study is targeted to identify of root specific genes expressed temporally and also gene(s) involved in lateral root and profuse root development. A total of 890 ESTs were identified from five EST libraries constructed using SSH approach which included temporal gene regulation (early and late) and genes involved in morphogenetic traits (lateral and profuse rooting). One hundred sixty-one unique ESTs identified from various libraries were categorized based on their putative functions and deposited in NCBI-dbEST database. In addition, 36 ESTs were selected for validation of their expression by RT-PCR. The present findings will help in shedding light to the unexplored developmental process of root growth in tomato and plant in general.

Primary structure of the soybean nodulin-35 gene encoding uricase II localized in the peroxisomes of uninfected cells of nodules

Nodulin-35 (N-35), a subunit of nodule-specific uricase (uricase II) of soybean (Glycine max), is shown to be preferentially synthesized on free polysomes during nodule development and is localized in peroxisomes of the uninfected cells of this tissue. A cDNA clone, isolated by using mRNA from immunoprecipitated polysomes, revealed the primary structure of this protein with a molecular mass of 35,100. That this clone represents N-35 was confirmed by comparing the deduced amino acid sequence with the partial sequence of a CNBr-cleaved peptide of purified N-35. Southern blot hybridizations with genomic DNA suggest that there are several EcoRI fragments containing N-35 sequences. Three of these sequences were isolated from a genomic library of soybean. Nucleotide sequence analysis showed that the complete gene extends almost 5000 base pairs on two EcoRI fragments and the coding region (309 codons) is interrupted by seven introns ranging in size from 154 to 1341 base pairs. Lack of a signal sequence and its translation on free polysomes suggest that N-35 is posttranslationally transported to the peroxisomes. Furthermore, there is no cross-hybridization of N-35 cDNA with RNA from young (3- to 4-day) roots and leaves, indicating that the observed "uricase" activity in these tissues is due to the product of a different gene.

Nodulin-24 gene of soybean codes for a peptide of the peribacteroid membrane and was generated by tandem duplication of a sequence resembling an insertion element

A nodulin gene coding for a polypeptide with an apparent M(r) of 24,000 (nodulin-24) was isolated from soybean (Glycine max). DNA sequence analysis of this gene revealed that its coding capacity is for a polypeptide of only M(r) 15,100 and is interrupted by four introns. The three middle exons and their flanking segments appear to have been generated by duplications of a unit resembling an insertion sequence. This unit is bounded by a 12-base-pair inverted repeat and encompasses the 54-base-pair exon corresponding to each of three central hydrophobic domains of the protein, nodulin-24. The resulting repeated hydrophobic structure of this protein may be responsible for an apparent increase in M(r) from 15,100 to 24,000. In vitro translation and immunological studies suggest that nodulin-24 is a precursor and is processed cotranslationally into a M(r) 20,000 polypeptide. This polypeptide is a component of the membrane envelope enclosing the bacteroids (peribacteroid membrane) synthesized during symbiosis with Rhizobium. The low degree (<6%) of sequence divergence among the repeated units suggests that this gene has been generated recently during the evolution of symbiotic nitrogen fixation in soybean.

Characterization of cDNA for nodulin-75 of soybean: A gene product involved in early stages of root nodule development

Establishment of a nitrogen-fixing root nodule is accompanied by a developmentally regulated expression of nodulin genes, only some of which, the so-called early nodulin genes, are expressed in stages preceding actual nitrogen fixation. We have isolated soybean cDNA clones representing early nodulin genes and have studied clone pENOD2 in detail. The cDNA insert of this clone hybridizes to nodule-specific RNA of 1200 nucleotides in length. The RNA that was hybrid-selected by the cloned ENOD2 DNA was in vitro translated to produce two nodulins with an apparent M(r) of 75,000, the N-75 nodulins. These two nodulins differ slightly in charge and one does not contain methionine. The amino acid sequence deduced from the DNA sequence shows that proline accounts for 45% of the 240 residues in these nodulins and the sequence contains at least 20 repeating heptapeptide units. The amino acid composition of none of the (hydroxy)proline-rich (glyco)proteins described in plants resembles the composition of the N-75 nodulins, especially with respect to the high glutamic acid and the low serine content. This suggests that the N-75 nodulins belong to a hitherto unidentified class of presumably structural proteins. The genes encoding the N-75 nodulins were found to be expressed in nodule-like structures devoid of intracellular bacteria and infection threads, indicating that these nodulins do not function in the infection process but more likely function in nodule morphogenesis.

Symbiotic Effectiveness and Host-Strain Interactions of Rhizobium fredii USDA 191 on Different Soybean Cultivars

Nodulation, acetylene reduction activity, dry matter accumulation, and total nitrogen accumulation by nodulated plants growing in a nitrogen-free culture system were used to compare the symbiotic effectiveness of the fast-growing Rhizobium fredii USDA 191 with that of the slow-growing Bradyrhizobium japonicum USDA 110 in symbiosis with five soybean (Glycine max (L.) Merr.) cultivars. Measurement of the amount of nitrogen accumulated during a 20-day period of vegetative growth (28 to 48 days after transplanting) showed that USDA 110 fixed 3.7, 39.1, 4.6, and 57.3 times more N(2) than did USDA 191 with cultivars Pickett 71, Harosoy 63, Lee, and Ransom as host plants, respectively. With the unimproved Peking cultivar as the host plant, USDA 191 fixed 3.3 times more N(2) than did the USDA 110 during the 20-day period. The superior N(2) fixation capability of USDA 110 with the four North American cultivars as hosts resulted primarily from higher nitrogenase activity per unit nodule mass (specific acetylene reduction activity) and higher nodule mass per plant. The higher N(2)-fixation capability of USDA 191 with the Peking cultivar as host resulted primarily from higher nodule mass per plant, which was associated with higher nodule numbers. There was significant variation in the N(2)-fixation capabilities of the four North American cultivar-USDA 191 symbioses. Pickett 71 and Lee cultivars fixed significantly more N(2) in symbiosis with USDA 191 than did the Harosoy 63 and Ransom cultivars. This quantitative variation in N(2)-fixation capability suggests that the total incompatibility (effectiveness of nodulation and efficiency of N(2) fixation) of host soybean plants and R. fredii strains is regulated by more than one host plant gene. These results indicate that it would not be prudent to introduce R. fredii strains into North American agricultural systems until more efficient N(2)-fixing symbioses between North American cultivars and these fast-growing strains can be developed. When inoculum containing equal numbers of USDA 191 and of strain USDA 110 was applied to the unimproved Peking cultivar in Perlite pot culture, 85% of the 160 nodules tested were occupied by USDA 191. With Lee and Ransom cultivars, 99 and 85% of 140 and 96 nodules tested, respectively, were occupied by USDA 110.

Differentiation of plant cells during symbiotic nitrogen fixation

Nitrogen-fixing symbioses between legumes and bacteria of the family Rhizobiaceae involve differentiation of both plant and bacterial cells. Differentiation of plant root cells is required to build an organ, the nodule, which can feed and accommodate a large population of bacteria under conditions conducive to nitrogen fixation. An efficient vascular system is built to connect the nodule to the root, which delivers sugars and other nutrients to the nodule and removes the products of nitrogen fixation for use in the rest of the plant. Cells in the outer cortex differentiate to form a barrier to oxygen diffusion into nodules, which helps to produce the micro-aerobic environment necessary for bacterial nitrogenase activity. Cells of the central, infected zone of nodules undergo multiple rounds of endoreduplication, which may be necessary for colonisation by rhizobia and may enable enlargement and greater metabolic activity of these cells. Infected cells of the nodule contain rhizobia within a unique plant membrane called the peribacteroid or symbiosome membrane, which separates the bacteria from the host cell cytoplasm and mediates nutrient and signal exchanges between the partners. Rhizobia also undergo differentiation during nodule development. Not surprisingly, perhaps, differentiation of each partner is dependent upon interactions with the other. High-throughput methods to assay gene transcripts, proteins, and metabolites are now being used to explore further the different aspects of plant and bacterial differentiation. In this review, we highlight recent advances in our understanding of plant cell differentiation during nodulation that have been made, at least in part, using high-throughput methods.

Transcripts for genes encoding soluble acid invertase and sucrose synthase accumulate in root tip and cortical cells containing mycorrhizal arbuscules

Arbuscule formation by the arbuscular mycorrhizal fungus Glomus intraradices (Schenck & Smith) was limited to cortical cells immediately adjacent to the endodermis. Because these cortical cells are the first to intercept photosynthate exiting the vascular cylinder, transcript levels for sucrose metabolizing-enzymes were compared between mycorrhizal and non-mycorrhizal roots. The probes corresponded to genes encoding a soluble acid invertase with potential vacuolar targeting, which we generated from Phaseolus vulgaris roots, a Rhizobium-responsive sucrose synthase of soybean and a cell wall acid invertase of carrot. Transcripts in non-mycorrhizal roots were developmentally regulated and abundant in the root tips for all three probes but in differentiated roots of P. vulgaris they were predominantly located in phloem tissues for sucrose synthase or the endodermis and phloem for soluble acid invertase. In mycorrhizal roots increased accumulations of transcripts for sucrose synthase and vacuolar invertase were both observed in the same cortical cells bearing arbuscules that fluoresce. There was no effect on the expression of the cell wall invertase gene in fluorescent carrot cells containing arbuscules. Thus, it appears that presence of the fungal hyphae in the fluorescent arbusculated cell stimulates discrete alterations in expression of sucrose metabolizing enzymes to increase the sink potential of the cell.

The temporal and spatial transcription pattern in root nodules of Vicia faba nodulin genes encoding glycine-rich proteins

Four different transcript sequences encoding gene products with an unusually high glycine content were identified in Vicia faba root nodules. Northern blot analysis revealed a strong nodule specific expression of the corresponding genes. Time course experiments showed that two of these genes were transcribed before the onset of leghemoglobin expression and hence were designated VfENOD-GRP2 and VfENOD-GRP5, whereas the first detection of VfNOD-GRP1 and VfNOD-GRP4 transcripts coincided with the appearance of leghemoglobin transcripts in V. faba root nodules. A characteristic feature of all encoded nodulins was a hydrophobic N-terminus, which in the case of the nodulins ENOD-GRP2 and ENOD-GRP5 has the characteristics of a signal peptide. Such a structure is comparable to other plant glycine-rich proteins decribed as components of the plant cell wall. Based on tissue print hybridizations, we found that VfNOD-GRP1, VfENOD-GRP2 and VfNOD-GRP4 were expressed in the interzone II-III and in the whole nitrogen-fixing zone III. In contrast to VfENOD-GRP2 and VfNOD-GRP4, the signal intensity of hybridizing VfNOD-GRP1 transcripts was slightly reduced in the more proximal part of broad bean root nodules. Apart from the interzone II-III and the nitrogen fixing zone III, VfENOD-GRP5 RNA was also detected in large areas of the prefixing zone II.

Characterization and gene expression of nodulin Npv30 from common bean

We previously reported that transcripts for a 30-kD nodulin (Npv30) are very abundant in the nodule. In this paper we describe the isolation and characterization of Npv30 cDNA and genomic clones. Npv30 has the following characteristic features: (a) a putative signal sequence at the deduced amino-terminal region, (b) a proline-rich stretch at the carboxy terminus, and (c) a characteristic domain of four cysteines that resemble metal-binding sites. In Phaseolus vulgaris L., Npv30 is encoded by a small gene family that shares discrete sequence homologies with another small gene family in soybean. An antibody against a beta-galactosidase-Npv30 fusion protein detected two proteins of 28 and 30 kD. Although Npv30 transcripts are very abundant, they encode proteins that are hardly detected in nodule fractions, suggesting that these proteins have a short half-life and/or the mRNAs are strongly regulated at the translational level. Npv30 transcripts were detected in the infected cells of the nodule by in situ hybridization experiments.

Morphological and Molecular Characteristics of Host-Conditioned Ineffective Root Nodules in Cowpea

In cowpea (Vigna unguiculata [L.] Walp.) a recessive allele, designated cpi, elicits the formation of non-N2-fixing nodules with all bacterial isolates tested. Comparisons of mutant and wild-type nodules demonstrated that the ineffective nodules were anatomically similar to the wild type and contained both infection threads and bacteroids. Ineffective nodules were smaller, however, largely because of the reduced size of the infected cells. Additionally, the number of bacteroids was reduced and senescence occurred prematurely in the infected cells. Grafting studies demonstrated that the defect in nodule development was controlled by the root rather than the shoot. Northern analysis of four nodulin genes indicated that in the ineffective nodules transcript levels of the early nodulin VuENOD2 were initially reduced but were equivalent to wild-type nodules by 21 d. In contrast, transcript levels of the early nodulin VuB were initially similar in both genotypes but as the nodules matured the mRNA levels declined more slowly in the ineffective nodules. The late nodulins leghemoglobin and uricase were expressed in the ineffective nodules but at greatly reduced levels. Thus, the cpi-conditioned defect in nodulation is associated with impaired bacteroid maturation and maintenance, altered nodulin expression, and accelerated senescence.

A survey of transcripts expressed specifically in root nodules of broadbean (Vicia faba L.)

More than 600 potentially nodule-specific clones have been detected by differential hybridization of a broadbean cDNA library constructed from root nodule poly(A)+ RNA. These isolated cDNAs belong to at least 28 different clone groups containing cross-hybridizing sequences. The number of clones within a clone group varies from about 200 to only one single clone. Northern hybridization experiments revealed nodule-specific transcripts for 14 clone groups and markedly nodule-enhanced transcripts for another 7 clone groups. Sequence homologies indicate that three transcript sequences code for different leghemoglobins. Two other transcripts encode a nodule-specific sucrose synthase and a nodule-enhanced asparagine synthetase, respectively. Four deduced gene products are proline-rich, two of them being the homologues of PsENOD2 and PsENOD12. The third proline-rich protein (PRP) is composed of similar amino acid repeats as the nodule-specific PsENOD12 but is expressed in nodules and roots in comparable amounts. The fourth PRP is a nodule-enhanced extensin-type protein built up by Ser-Pro4 repeats. Two further nodule-specific transcripts encode gene products showing some similarity to structural glycine-rich proteins. Additionally, transcripts could be identified for broadbean homologues of the nodulins MsNOD25, PsENOD3 and PsENOD5 and transcripts specifying a nodule-enhanced lipoxygenase and a translation elongation factor EF-1 alpha, which is expressed in all broadbean tissues tested.

Towards an integrated linkage map of common bean 2. Development of an RFLP-based linkage map

A restriction fragment length polymorphism (RFLP)-based linkage map for common bean (Phaseolus vulgaris L.) covering 827 centiMorgans (cM) was developed based on a F2 mapping population derived from a cross between BAT93 and Jalo EEP558. The parental genotypes were chosen because they exhibited differences in evolutionary origin, allozymes, phaseolin type, and for several agronomic traits. The segregation of 152 markers was analyzed, including 115 RFLP loci, 7 isozyme loci, 8 random amplified polymorphic DNA (RAPD) marker loci, and 19 loci corresponding to 15 clones of known genes, 1 virus resistance gene, 1 flower color gene, and 1 seed color pattern gene. Using MAPMAKER and LINKAGE-1, we were able to assign 143 markers to 15 linkage groups, whereas 9 markers remained unassigned. The average interval between markers was 6.5 cM; only one interval was larger than 30 cM. A small fraction (9%) of the markers deviated significantly from the expected Mendelian ratios (1∶2∶1 or 3∶1) and mapped into four clusters. Probes of known genes belonged to three categories: seed proteins, pathogen response genes, and Rhizobium response genes. Within each category, sequences homologous to the various probes were unlinked. The I gene for bean common mosaic virus resistance is the first disease resistance gene to be located on the common bean genetic linkage map.

Biosynthesis and Secretion of Cryptogein, a Protein Elicitor Secreted by Phytophthora cryptogea

The phytopathogenic fungi Phytophthora subspecies elicit hypersensitive-like necroses on their nonhost tobacco (Nicotiana tabacum), with the exception of the tobacco pathogen Phytophthora nicotianae. In culture, these fungi-except P. nicotianae-secrete proteins, called elicitins, that cause these remote leaf necroses and are responsible for the incompatible reaction. These proteins protect tobacco against invasion by the agent of the tobacco black shank, P. nicotianae, which is unable to produce such an elicitor. Cryptogein, secreted by Phytophthora cryptogea, has been purified, sequenced, and characterized as an elicitin, a novel family of 10 kilodalton holoproteins. In the present paper, we examined the secretion and biosynthesis of this protein elicitor from P. cryptogea culture. Results showed that the secretion of cryptogein began later than its synthesis and stopped earlier, simultaneously with mycelium growth, when the nitrogen source in the culture medium was nearly exhausted. Electrophoretic patterns of total protein from mycelium extracts and N-terminal sequence analysis showed that cryptogein accumulated in the mycelium in its mature form. The comparison of the immunoselected in vitro translation products with (35)S in vivo-labeled cryptogein showed that cryptogein was synthesized as a preprotein with a signal peptide removed cotranslationally before the secretion into the culture medium. Immunoselected in vitro-synthesized products were subjected to radiosequencing to clearly determine the N-terminal position and the size (20 amino acids) of the signal peptide. Cryptogein did not undergo any other posttranslational modification.

Characterization and genomic organization of a highly expressed late nodulin gene subfamily in soybeans

A soybean nodulin cDNA clone (E41) hybrid-selected mRNA for three in vitro translation products with apparent molecular weights of 26 kDa, 25 kDa and 24 kDa. Based on Southern analysis of soybean genomic DNA, combined with mapping and sequencing of genomic clones, we identified four genes that are related to E41, one of which was identified to be the previously characterized N-20 gene. Our data indicate the linkage of three of the genes, of which one is a truncated version and suggest that they originated by gene duplication combined with deletion and conversion. The genes are highly expressed and we postulate that the sequence conservation in the 5' and 3' flanking regions of all four genes, has a functional role in their expression. Hybrid-selected translation products of E41 are not immunoprecipitable with antibody to the soluble fraction of nodules suggesting that they are membrane associated. The N-20 gene, which is a member of this gene subfamily, showed sequence similarity to four previously characterized nodulin genes and a phylogenetic tree is proposed based on the extent of sequence similarity.

Oxygen regulation of uricase and sucrose synthase synthesis in soybean callus tissue is exerted at the mRNA level

The effect of lowering oxygen concentration on the expression of nodulin genes in soybean callus tissue devoid of the microsymbiont has been examined. Poly(A)+ RNA was isolated from tissue cultivated in 4% oxygen and in normal atmosphere. Quantitative mRNA hybridization experiments using nodule-specific uricase (Nodulin-35) and sucrose synthase (Nodulin-100) cDNA probes confirmed that the synthesis of the uricase and sucrose synthase is controlled by oxygen at the mRNA level. The steady-state levels of uricase and sucrose synthase mRNA increased significantly (5-6- and 4-fold respectively) when the callus tissue was incubated at reduced oxygen concentration. Concomitant with the increase in mRNA level a 6-fold increase in specific activity of sucrose synthase was observed. Two messengers representing poly-ubiquitin precursors also responded to lowering the oxygen concentration. The increase was about 5-fold at 4% oxygen. No expression at atmospheric oxygen or in response to low oxygen was observed when using cDNA probes for other nodulin genes such as leghemoglobin c3, nodulin-22 and nodulin-44.

Isolation of transcriptionally regulated root-specific genes from tobacco

Four root-specific cDNA clones and their corresponding genomic clones have been isolated from tobacco (Nicotiana tabacum) by a novel differential hybridization procedure. The genes are expressed at high levels in roots and are not detectable in leaves. The cDNAs are encoded by small gene families of two to four members. Transcription experiments with isolated nuclei demonstrate that the genes are, at least in part, transcriptionally regulated. Constructions in which 1.4 kilobase pairs of 5' flanking region of one of the root-specific genes was fused to a reporter gene (beta-glucuronidase) were transformed into tobacco. beta-Glucuronidase activity in transgenic plants was localized in the roots, demonstrating the cis-acting sequences regulating root-specific expression are present on the 5' flanking region.

Plant gene expression during effective and ineffective nodule development of the tropical stem-nodulated legume Sesbania rostrata

The expression of plant genes during symbiosis of Sesbania rostrata with Rhizobium sp. and Azorhizobium caulinodans was studied by comparing two-dimensional PAGE patterns of in vitro translation products of poly(A)(+) RNA from uninfected roots and stems with that of root and stem nodules. Both types of nodules are essentially similar, particularly when stem nodules are formed in the dark. We detected the specific expression of at least 16 genes in stem and root nodules and observed the stimulated expression of about 10 other genes in both nodules. Six of the nodule-specific translation products (apparent molecular masses around 16 kDa) cross-react with an antiserum raised against leghemoglobin purified from Sesbania rostrata stem nodules. During stem nodule development, most of the nodule-stimulated genes are expressed concomitantly with leghemoglobin at day 12 after inoculation. However, some genes are already stimulated at days 6-7, some others later in development (day 18), and some are transiently activated. Patterns of root nodules induced by either Azorhizobium caulinodans strain ORS571, capable of effective root and stem nodulation, or Rhizobium sp. strain ORS51, capable of effective root nodulation only, are very similar except for a specific 37.5 kDa polypeptide. Several types of ineffective stem and root nodules were studied; in every case the amount of leghemoglobin components appeared reduced together with most of the nodule-stimulated polypeptides.

Expression of nodule-specific genes in Phaseolus vulgaris L

The identification of some nodule-specific host proteins (nodulins) from common bean (Phaseolus vulgaris L.), a tropical ureide-transporting legume, is described. Particularly, the existence and developmental expression of several abundant nodule-specific transcripts of P. vulgaris are shown, including leghemoglobin, nodulespecific uricase and a group that in vitro translates into a cluster of about 30 kDa products. The expression pattern of nodulins in effective (Fix(+)) nodules compared to ineffective (Fix(-)) ones is also presented. The modified expression of main nodulins observed between these nodules indicates that different levels and/or factors associated with their regulation are involved. The intracellular infection by Rhizobium as a decisive step in the induction of some P. vulgaris nodulins is discussed.

Appearance of purine-catabolizing enzymes in fix and fix root nodules on soybean and effect of oxygen on the expression of the enzymes in callus tissue

The appearance of enzymes involved in the formation of ureides, allantoin, and allantoic acid, from inosine 5'-monophosphate was analyzed in developing root nodules of soybean (Glycine max). Concomitant with development of effective nodules, a substantial increase in specific activities of the enzymes 5'-nucleotidase (35-fold), purine nucleosidase (10-fold), xanthine dehydrogenase (25-fold), and uricase (200-fold), over root levels was observed. The specific activity of allantoinase remained constant during nodule development. With ineffective nodules the activities were generally lower than in effective nodules; however, the activities of 5'-nucleotidase and allantoinase were 2-fold higher in ineffective nodules unable to synthesize leghemoglobin than in effective nodules. Since the expression of uricase has been shown to be regulated by oxygen (K Larsen, BU Jochimsen 1986 EMBO J 5: 15-19), the expression of the remaining enzymes in the purine catabolic pathway were tested in response to variations in O(2) concentration in sterile soybean callus tissue. Purine nucleosidase responded to this treatment, exhibiting a 4-fold increase in activity around 2% O(2). 5'-Nucleotidase, xanthine dehydrogenase, and allantoinase remained unaffected by variations in the O(2) concentration. Hence, the expression of two enzymes involved in ureide formation, purine nucleosidase and uricase, has been demonstrated to be influenced by O(2) concentration.

Plant gene expression in effective and ineffective root nodules of alfalfa (Medicago sativa)

Expression of plant genes involved in the symbiosis between alfalfa (Medicago sativa) and Rhizobium meliloti has been studied by comparing root and root nodule mRNA populations. Two-dimensional gel electrophoretic separation of the in vitro translation products of polyA(+) RNA isolated from either roots or effective root nodules has allowed us to identify thirteen nodule-specific translation products, including those corresponding to the leghemoglobins (Lb). These translation products, representing putative nodulin mRNAs, are first detected between 9 and 12 days after inoculation, a result which has been confirmed for Lb mRNA by Northern blotting and hybridization with a Lb cDNA probe. Analysis of three different types of ineffective root nodules arrested in different stages of development has led to the following conclusions. (i) The transcription of eleven nodule-specific genes, including the Lb genes, is independent of nitrogen-fixing activity. (ii) Differentiation of the primary nodule structure does not require the transcription of any of these genes but can be correlated with a dramatic reduction in the level of at least five transcripts present in the root. (iii) There is enhanced expression of certain plant genes in the case of nodules elicited by an Agrobacterium strain carrying the symbiotic plasmid of R. meliloti.

Nodulin gene expression during soybean (Glycine max) nodule development

In vitro translation products of total RNA isolated from soybean nodules at successive stages of nodule development were analyzed by two-dimensional gel electrophoresis. In that way the occurrence of over 20 mRNAs specifically transcribed from nodulin genes was detected. The nodulin genes could be divided into two classes according to the time of expression during nodule development. Class A comprises at least 4 nodulin mRNAs which are found when a globular meristem is present in the root cortex. These class A nodulin genes have a transient expression. Class B nodulin genes are expressed when the formation of a nodule structure has been completed. Bradyrhizobium japonicum nod (+) fix(-)mutants, with large deletions spanning the nif H,DK region, still induced nodules showing normal expression of all nodulin genes, indicating that the nif H,DK region is not involved in the induction of nodulin genes. In nodules induced by Bradyrhizobium japonicum nod (+) fix(-)mutant HS124 the bacteria are rarely released from the infection thread and the few infected cells appear to be collapsed. All class A and class B nodulin genes are expressed in HS124 nodules with the exception of 5 class B genes.

A block in the endocytosis of Rhizobium allows cellular differentiation in nodules but affects the expression of some peribacteroid membrane nodulins

A transposon-induced mutant (T8-1) of Bradyrhizobium japonicum (61A76) was unable to develop into the nitrogen-fixing endosymbiotic form, the bacteroid. Comparison between this mutant and T5-95, an ineffective (non-nitrogen fixing, Fix(-)) mutant, confirmed that the process of bacteroid development is a distinct phase of differentiation of the endosymbiont and is independent of nitrogen fixation activity. The T8-1 mutant was able to induce normal-size nodules which differentiated two plant cell types and contained numerous infection threads. However, the infected cells were devoid of bacteroids. Electron microscopy revealed that the ends of the infection threads were broken down in a normal manner once the thread had penetrated the cells, but the mutant was not internalized by endocytosis. The lack of peribacteroid membrane (PBM) in nodules induced by this mutant was correlated with a reduced level of expression of plant genes coding for PBM nodulins. These genes were expressed in the T5-95 mutant, showing that the low expression in T8-1 was not due to the lack of nitrogen fixation. One of the PBM nodulins, nodulin-26, was found at normal levels in the nodules which lack PBM, suggesting that there are at least two developmental stages in PBM biosynthesis. These data suggest that a coordination of plant and Rhizobium gene expression is required for the release and internalization of bacteria into the PBM compartments of infected cells of nodules.

Several nodulins of soybean share structural domains but differ in their subcellular locations

Four soybean cDNA nodule-specific clones encoding nodulin-23, -26b, -27 and -44 were observed to cross-hybridize under low stringency conditions. Nucleotide sequence analysis revealed that the cDNAs contain three distinct domains: two domains with 70 to 95% homology separated by a third domain unique to each cDNA. Despite a number of nucleotide insertions and deletions, the protein sequences are conserved in the two domains which correlate with the homologous nucleotide domains. The amino terminal domain of each nodulin contains putative signal sequences for membrane translocation, although only two (nodulin-23 and -44) meet all the criteria for a functional signal. Immuno-precipitation of hybrid-release translation products of the four cDNAs revealed that nodulin-23 is associated with the peribacteroid membrane while nodulin-27 is in the cytoplasmic fraction of the nodule. These four nodulins are members of a diverse family with conserved structural features and the genes encoding them appear to have recently evolved from a common ancestor.

Gene expression in the soybean seed axis during germination and early seedling growth

Copy-DNA clones have been obtained that distinguish eight messenger mRNAs, moderately abundant in the axes of the germinating soybean (Glycine max (L.) Merr.) seedling. These clones have been used to characterize the size of the mRNAs and to anlyze the accumulation of the mRNAs at different time points and in different parts of the axis during germination and early seedling growth. Three of the mRNAs accumulate to a substantial level by 9 h, a time point before either the beginning of growth or the accumulation of polyribosomes. Four other mRNAs reach a substantial level only at 24 h, a period when rapid seedling growth is occurring. Those mRNAs whose accumulation begins at 24 h were found only in the top (hypocotyl) half of the 24-h seedlings, while the remaining mRNAs were present also in the bottom half of the seedlings in different amounts. By 44 h, the bottom 0.5 cm of the seedlings, i.e., the region of meristematic growth, had little or none of the mRNAs, with the exception of one mRNA. These temporal and spatial observations indicate that many of the mRNAs are not involved simply in the general maintenance of ongoing cell proliferation, but that they may be related to differentiation during early seedling formation. Further, the early accumulating mRNAs may be functioning in regulating the onset of seedling growth.

Nodulin-26, a peribacteroid membrane nodulin is expressed independently of the development of the peribacteroid compartment

The peribacteroid membrane (pbm) of root nodules is derived from the plant cell plasma membrane but contains in addition several nodule-specific host proteins (nodulins). Antibodies raised against purified pbm of soybean were used to immunoprecipitate polysomes to isolate an RNA fraction that served as a template for the synthesis of a cDNA probe for screening a nodule-specific cDNA library. Clone p1B1 was found to encode a 26.5 kDa polypeptide (nodulin-26) which is immunoprecipitable specifically with the anti-pbm serum. Nodulin-26 has features of a transmembrane protein and its structure differs from that of nodulin-24 which appears to be a surface protein of pbm. The expression of these two pbm nodulins was examined in nodules induced by Bradyrhizobium japonicum Tn5 mutants that arrest nodule development at different stages of pbm biosynthesis. Nodules that do not show release of bacteria from the infection thread express nodulin-24 at a very low level. In contrast, the expression of nodulin-26 occurs fully in nodules that form infection threads only and is not affected by the release of bacteria from the threads.

Nodulins and nodulin genes of Glycine max

Nodulins are organ-specific plant proteins induced during symbiotic nitrogen fixation. Nodulins play both metabolic and structural roles within infected and uninfected nodule cells. In soybean, several nodulin genes, coding for abundant nodulins, have been identified and isolated. Structural analysis of some of these genes has revealed their possible mode of regulation and the subcellar location of the protein product. Studies of ineffective symbiosis based on cultivar-strain genotype differences suggested that both partners influence the expression of nodulin genes. Concomitant with nodule organogenesis, the Rhizobium undergoes substantial differentiation leading to the accumulation of nodule-specific bacterial proteins, bacteroidins. The major structural alteration occuring in the infected cell is the formation of a membrane enclosing the bacteroid (peribacteroid membrane). A number of nodulins are specifically targetted to this membrane during endosymbiosis. The induction of nodulins and bacteroidins leads to the formation of an effective nodule. Nodulin genes can be induced in vitro by factors derived from nodules suggesting that trans-activators may be involved in derepression of the host genes necessary for Rhizobium-legume symbiosis.

Leghemoglobin-like sequences in the DNA of four actinorhizal plants

A cloned cDNA partial copy of a soybean leghemoglobin mRNA was used to probe genomic DNA of four species of actinorhizal plants. Southern blot hybridization revealed the presence of sequences with homology to the leghemoglobin probe in DNA from Alnus glutinosa, Casuarina glauca, Ceanothus americanus and Elaeagnus pungens. The hybridization patterns of the restriction fragments revealed some fragment size conservation between the DNA of soybean and the DNA of four actinorhizal plants which are taxonomically unrelated to soybean or to each other. The results presented here indicate that globin gene sequences are much more widely distributed in the plant kingdom than has previously been thought. Furthermore, if sequence conservation is actually as high as the restriction fragment patterns suggest, the evolution of the DNA surrounding the globin sequences has been highly constrained.

Promoter analysis of a soybean nuclear gene coding for nodulin-23, a nodule-specific polypeptide involved in symbiosis with Rhizobium

Soybean nodulin-23 gene, induced in nodules formed due to symbiosis with Rhizobium, was found to contain multiple sequences capable of acting as eucaryotic and procaryotic promoters. The transcription start sites of this gene were localized by S1 nuclease mapping, primer extension with nodule mRNA and in vitro run-off transcription analysis. A major transcription start site was observed by S1 mapping; however, the the primer extension revealed a second start site. Sequence analysis showed the presence of tandemly arranged eucaryotic promoter sequences, each corresponding to one of the observed transcription start sites. In vitro transcription analysis with HeLa cell extract demonstrated the presence of another alpha-amantin-sensitive transcript ('anti-sense') with its direction opposite to that of the nodulin mRNA. The 5' ends for 80 nucleotides of nodulin and 'anti-sense' messages are complementary to each other. In addition, three tandemly arranged, functional procaryotic promoters (assayed in Escherichia coli) are found to be located within the eucaryotic promoter sites is similar to that of the major in vivo transcript in nodules. The potential significance for the presence of several promoter-like sequences in this gene is discussed.

The detection of leghemoglobin-line sequences in legumes and non-legumes

Leghemoglobin is a major component of the nitrogen-fixing nodules formed by legumes in association with bacterial symbionts of the genusRhizobium. It is thought to be involved in regulating the oxygen tension within nodules. In a series of Southern blot experiments using cloned soybean leghemoglobin cDNAs as hybridization probes, cross-hybridizing sequences have been detected in legumes closely related to soybean (members of the Leguminosae subfamily Papilionoideae), as well as in a distantly related legume not reported to be nodulated (subfamily Caesalpinioideae). With the same probes, the presence of cross-hybridizing sequences has also been detected in plants outside the Leguminosae, including two nitrogen-fixing non-legumes and one species which is not nodulated. These results suggest that the genes for oxygen-binding proteins may be more widely dispersed than previously thought.

Expression of plant genes during the development of pea root nodules

The expression of plant genes involved in the pea-Rhizobium symbiosis was studied by analysing mRNA from root nodules. The RNA was translated in vitro and the translation products were separated by two-dimensional gel electrophoresis. The results show differential expression of nodulin genes during root nodule development. One gene encoding N-40' is expressed at a significant level 5 days before the leghemoglobin genes. Most other nodulin genes are expressed more of less concomitantly with the leghemoglobin genes whereas the N-21 mRNA is only present late during the development. In the development of ineffective root nodules induced by infection with different nod+fix- mutants of R. leguminosarum all nodulin genes are expressed except for the N-21 gene. The results suggest that neither bacteroid development, heme excretion nor nitrogen fixation are essential for the induction of nodulin gene expression in the host plant. Further, it appears that the amount of leghemoglobin in ineffective nodules is regulated at a post-transcriptional level.

Primary structure of the soybean nodulin-23 gene and potential regulatory elements in the 5'-flanking regions of nodulin and leghemoglobin genes

The nodulin-23 gene of soybean is one of the most abundantly transcribed genes induced during symbiosis with Rhizobium. Using a plasmid (pNod25) from a nodule cDNA library, we have isolated the nodulin-23 gene from a soybean genomic library. Nucleotide sequence analysis of the cDNA and of the genomic clone indicated that the coding region of this gene is 669 bp long and is interrupted by a single intron of about 530 bp. The deduced protein sequence suggests that nodulin-23 may have a signal sequence. The 5'-flanking sequence of two other nodulin genes, nodulin-24 encoding for a membrane polypeptide and one of the leghemoglobin genes (LbC3), were obtained. Comparison of these sequences revealed three conserved regions, one of which, an octanucleotide (GTTTCCCT), has 100% homology. The conserved sequences are arranged in a unique fashion and have a spatial organization with respect to order and position, which may suggest a potential regulatory role in controlling the expression of nodulin and leghemoglobin genes during symbiosis.

Appearance and accumulation of nodulin mRNAs and their relationship to the effectiveness of root nodules

Cloned cDNAs corresponding to mRNAs which accumulate in nitrogen-fixing root nodules of soybean (nodulin mRNAs) were used as probes to investigate the sizes, sequence relationships, tissue specificities and developmental accumulations of individual nodulin mRNA sequences. Northern blot analysis indicated that the NodB, NodC and NodD mRNA sequences are 1 150, 770, and 3 150 nucleotides long, respectively, which is consistent with the previously determined sizes of the hybrid-selected translation products (27 000, 24 000 and 100 000 MW, respectively). The NodA clones pNodA15 and pNodA25 hybridized to two mRNAs of lengths 1 600 and 1 100 nucleotides, indicating that they contain significant sequence homologies. However, increasing the hybridization stringency showed that the pNodA15 clone encodes the 1 600 nucleotide mRNA corresponding to the major NodA hybrid-selected translation product (44 000 MW) while pNodA25 encodes an mRNA of 1 100 nucleotides. The latter probably corresponds to one of two smaller (23 500 and 24 500 MW) in vitro translation products. RNA dot-blot hybridizations indicated that nodulin and leghemoglobin mRNAs began to appear and accumulate in Rhizobium infected root tissue very early (day 3 to 5) and reached fully induced levels by day 11. This accumulation was specific for nodule tissue (except for the NodD sequence) and preceded the accumulation of nitrogen fixation activity. Nodules produced by different effective Rhizobium strains accumulated similar levels of leghemoglobin and nodulin mRNAs while ineffective strains had a pleiotropic affect. While one ineffective strain (61A24) gave reduced levels of all these mRNAs, the other (SM5) gave levels which were nearly normal by the time nitrogen fixation activity should have reached its maximal level (day 17). Thus, leghemoglobin and nodulin genes are switched on soon after infection, prior to nodule morphogenesis, and the switch occurs prior to and is independent of nitrogen fixation activity.

Chromosomal arrangement of leghemoglobin genes in soybean

A cluster of four different leghemoglobin (Lb) genes was isolated from AluI-HaeIII and EcoRI genomic libraries of soybean in a set of overlapping clones which together include 45 kilobases (kb) of contiguous DNA. These four genes, including a pseudogene, are present in the same orientation and are arranged in the order: 5'-Lba-Lbc1-Lb psi-Lbc3-3'. The intergenic regions average 2.5 kb. In addition to this main Lb locus, there are other Lb genes which do not appear to be contiguous to this locus. A sequence probably common to the 3' region of Lb loci was found flanking the Lbc3 gene. The 3' flanking region of the main Lb locus also contains a sequence that appears to be expressed more abundantly in root tissue. Another sequence which is primarily expressed in root and leaf is found 5' to two Lb loci. Overall, the main leghemoglobin locus is similar in structure to the mammalian globin gene loci.