The primary structures of two leghemoglobin genes from soybean

Uncovering the roles of hemoglobins in soybean facing water stress

Water stress drastically hinders crop yield, including soybean - one of the world's most relevant feeding crops - threatening the food security of an ever-growing global population. Hemoglobins (GLBs) are involved in water stress tolerance; however, the role they effectively play in soybean remains underexplored. In this study, in silico and in vivo analyses were performed to identify soybean GLBs, capture their transcriptional profile under water stress, and overexpress promising members to assess how soybean cope with waterlogging. Seven GLBs were found, two GLB1 (non-symbiotic) and five GLB2 (symbiotic or leghemoglobins). Three out of the seven GLBs were differentially expressed in soybean RNA-seq libraries of water stress and were evaluated by real-time PCR. Consistently, GmGLB1-1 and GmGLB1-2 were moderately and highly expressed under waterlogging, respectively. Composite plants with roots overexpressing GmGLB1-1 or GmGLB1-2 (mostly) showed higher transcript abundance of stress-defensive genes involved in anaerobic, nitrogen, carbon, and antioxidant metabolism when subjected to waterlogging. In addition, soybean bearing p35S:GmGLB1-2 had lower H2O2 root content, a reactive oxygen species (ROS), under water excess compared with the control condition. Altogether these results suggest that GmGLB1-2 is a strong candidate for soybean genetic engineering to generate waterlogging-tolerant soybean cultivars.

Expression of soybean plant hemoglobin gene family under abiotic stresses

Many abiotic stresses induce the generation of nitric oxide (NO) in plant tissues, where it functions as a signal molecule in stress responses. Plants modulate NO by oxidizing it to NO₃ ^- with plant hemoglobin (GLB), because excess NO is toxic to cells. At least eight genes encoding GLB have been identified in soybean, in three clades: GLB1, GLB2, and GLB3. However, it is still unclear which GLB genes are responsible for NO regulation under abiotic stress in soybean. We exposed soybean roots to flooding, salt, and two NO donors-sodium pentacyanonitrosylferrate (III) dihydrate (SNP) and S-nitroso-N-acetyl-d,l-penicillamine (SNAP)-and analyzed expression of GLB genes. GmGLB1, one of two GLB1 genes of soybean, significantly responded to both SNP and SNAP, and its induction was almost completely repressed by a NO scavenger, 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide. GmGLB1 responded to flooding but not to salt, suggesting that it is responsible for NO regulation under NO-inducing abiotic stresses such as flooding. GmGLB3, one of two GLB3 genes of soybean, did not respond to NO donors at all but did respond to flooding, at a lower level than GmGLB1. These results suggest that flooding induces not only NO but also unknown factor(s) that induce GmGLB3 gene in soybean.

Hemoglobin in a nonleguminous plant, parasponia: possible genetic origin and function in nitrogen fixation

A dimeric hemoglobin was purified from nitrogen-fixing root nodules formed by association of Rhizobium with a nonleguminous plant, Parasponia. The oxygen dissociation rate constant is probably sufficiently high to allow Parasponia hemoglobin to function in a fashion similar to that of leghemoglobin, by oxygen buffering and transport during symbiotic nitrogen fixation. The identification of hemoglobin in a nonlegume raises important questions about the evolution of plant hemoglobin genes.

Complete nucleotide sequence of a French bean storage protein gene: Phaseolin

The complete nucleotide sequences of the gene and the mRNA coding for a specific phaseolin type French bean major storage protein have been determined. Comparison of these sequences reveals a phaseolin gene structure consisting of 80 base pairs (bp) of 5' untranslated DNA, 1,263 bp of protein-encoding DNA which is interrupted by five intervening sequences (IVS1, 72 bp; IVS2, 88 bp; IVS3, 124 bp; IVS4, 128 bp; and IVS5, 103 bp), and 135 bp of 3' untranslated DNA. Sequences characteristic of eukaryotic promoters "CCAAT" and "TATA" are present in the 5' flanking DNA, and the eukaryotic poly(A) addition signal A-A-T-A-A-A occurs 16 bp before the first nucleotide of poly(A). The derived amino acid sequence yields an amino acid composition and a molecular weight compatible with those found for the beta-type phaseolin protein. Two regions that probably serve as carbohydrate-peptide linkage recognition sites have been identified. A region of highly hydrophobic amino acids at the NH(2) terminus of the protein suggests the presence of a signal peptide in the newly synthesized phaseolin protein.

Expression of a complete soybean leghemoglobin gene in root nodules of transgenic Lotus corniculatus

The complete soybean leghemoglobin lbc(3) gene was transferred into the legume Lotus corniculatus using an Agrobacterium rhizogenes vector system. Organ-specific expression of the soybean gene was observed in root nodules formed on regenerated transgenic plants after infection with Rhizobium loti. The primary transcript was processed in the same way as in soybean nodules and the resulting mRNA was translated into Lbc(3) protein. Quantitative determination of the Lbc(3) protein in nodules of transgenic plants indicated that the steady-state level of the soybean protein is comparable to that of endogenous Lotus leghemoglobin.

Plant hemoglobins: what we know six decades after their discovery

This review describes contributions to the study of plant hemoglobins (Hbs) from a historical perspective with emphasis on non-symbiotic Hbs (nsHbs). Plant Hbs were first identified in soybean root nodules, are known as leghemoglobins (Lbs) and have been characterized in detail. It is widely accepted that a function of Lbs in nodules is to facilitate the diffusion of O(2) to bacteroids. For many years Hbs could not be identified in plants other than N(2)-fixing legumes, however in the 1980s a Hb was isolated from the nodules of the non-legume dicot plant Parasponia, a hb gene was cloned from the non-nodulating Trema, and Hbs were detected in nodules of actinorhizal plants. Gene expression analysis showed that Trema Hb transcripts exist in non-symbiotic roots. In the 1990s nsHb sequences were also identified in monocot and primitive (bryophyte) plants. In addition to Lbs and nsHbs, Hb sequences that are similar to microbial truncated (2/2) Hbs were also detected in plants. Plant nsHbs have been characterized in detail. These proteins have very high O(2)-affinities because of an extremely low O(2)-dissociation constant. Analysis of rice Hb1 showed that distal His coordinates heme Fe and stabilizes bound O(2); this means that O(2) is not released easily from oxygenated nsHbs. Non-symbiotic hb genes are expressed in specific plant tissues, and overexpress in organs of stressed plants. These observations suggest that nsHbs have functions additional to O(2)-transport, such as to modulate levels of ATP and NO.

A single hemoglobin gene in Myrica gale retains both symbiotic and non-symbiotic specificity

Here, a hemoglobin gene from the nitrogen-fixing actinorhizal plant Myrica gale was isolated, cloned and sequenced. The gene (MgHb) was a class I hemoglobin with strong sequence homology to non-symbiotic hemoglobin genes. MgHb is highly expressed in symbiotic root nodules, but transcripts and protein were also detected in leaves of M. gale. In Arabidopsis thaliana the MgHb promoter, linked to a beta-glucuronidase coding region, directed expression in the vascular tissue, in shoot meristem and at root branch point--a pattern very similar to the combined expression pattern of the two non-symbiotic A. thaliana hemoglobin promoters AHb1 and AHb2. The results points to a symbiotic as well as a non-symbiotic specificity of MgHb similar to a hemoglobin gene identified in Parasponia andersonii, but different from the situation in Casuarina glauca--a close actinorhizal relative of M. gale.

A ubiquitously expressed human hexacoordinate hemoglobin

We have identified a new human hemoglobin that we call histoglobin because it is expressed in a wide array of tissues. Histoglobin shares less than 30% identity with the other human hemoglobins, and the gene contains an intron in an unprecedented location. Spectroscopic and kinetic experiments with recombinant human histoglobin indicate that it is a hexacoordinate hemoglobin with significantly different ligand binding characteristics than the other human hexacoordinate hemoglobin, neuroglobin. In contrast to the very high oxygen affinities displayed by most hexacoordinate hemoglobins, the biophysical characteristics of histoglobin indicate that it could facilitate oxygen transport. The discovery of histoglobin demonstrates that humans, like plants, differentially express multiple hexacoordinate hemoglobins.

N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence

Myristoylation by the myristoyl-CoA:protein N-myristoyltransferase (NMT) is an important lipid anchor modification of eukaryotic and viral proteins. Automated prediction of N-terminal N-myristoylation from the substrate protein sequence alone is necessary for large-scale sequence annotation projects but it requires a low rate of false positive hits in addition to a sufficient sensitivity. Our previous analysis of substrate protein sequence variability, NMT sequences and 3D structures has revealed motif properties in addition to the known PROSITE motif that are utilized in a new predictor described here. The composite prediction function (with separate ad hoc parameterization (a) for queries from non-fungal eukaryotes and their viruses and (b) for sequences from fungal species) consists of terms evaluating amino acid type preferences at sequences positions close to the N terminus as well as terms penalizing deviations from the physical property pattern of amino acid side-chains encoded in multi-residue correlation within the motif sequence. The algorithm has been validated with a self-consistency and two jack-knife tests for the learning set as well as with kinetic data for model substrates. The sensitivity in recognizing documented NMT substrates is above 95 % for both taxon-specific versions. The corresponding rate of false positive prediction (for sequences with an N-terminal glycine residue) is close to 0.5 %; thus, the technique is applicable for large-scale automated sequence database annotation. The predictor is available as public WWW-server with the URL http://mendel.imp.univie.ac.at/myristate/. Additionally, we propose a version of the predictor that identifies a number of proteolytic protein processing sites at internal glycine residues and that evaluates possible N-terminal myristoylation of the protein fragments.A scan of public protein databases revealed new potential NMT targets for which the myristoyl modification may be of critical importance for biological function. Among others, the list includes kinases, phosphatases, proteasomal regulatory subunit 4, kinase interacting proteins KIP1/KIP2, protozoan flagellar proteins, homologues of mitochondrial translocase TOM40, of the neuronal calcium sensor NCS-1 and of the cytochrome c-type heme lyase CCHL. Analyses of complete eukaryote genomes indicate that about 0.5 % of all encoded proteins are apparent NMT substrates except for a higher fraction in Arabidopsis thaliana ( approximately 0.8 %).

Short-term metabolic responses of soybean root nodules to nitrate

Soybean (Glycine max L. Merr.) plants exposed to 10 mM KNO(3) for a 4 d period were used to test the correlation between nitrogenase activity, gene expression and sucrose metabolism. Nitrate caused the down-regulation of sucrose synthase (SS) transcripts within 1 d, although a decline in nodule SS activity and an increase in nodule sucrose content only occurred after 3-4 d. In a second experiment, plants were exposed to (15)N-labelled nitrate for 48 h to determine the time period during which nitrate was taken up, and to relate this to the decline in apparent nitrogenase activity (H(2) production in air) and the reduction in SS gene transcript levels. The peak of nitrate uptake appeared to be between 8 h and 14 h whilst apparent nitrogenase activity began to decline at about 17.5 h. The SS mRNA signal declined markedly between 14 h and 24 h. The correlative association of these factors is clear. However, SS activity per se does not appear to be related to the initial decline in apparent nitrogenase activity as a result of nitrate uptake. These findings, therefore, do not support the hypothesis that the regulation of nodule function is mediated by the regulation of SS activity.

Molecular cloning, functional characterization, and subcellular localization of soybean nodule dihydrolipoamide reductase

Nodule ferric leghemoglobin reductase (FLbR) and leaf dihydrolipoamide reductase (DLDH) belong to the same family of pyridine nucleotide-disulfide oxidoreductases. We report here the cloning, expression, and characterization of a second protein with FLbR activity, FLbR-2, from soybean (Glycine max) nodules. The cDNA is 1,779 bp in length and codes for a precursor protein comprising a 30-residue mitochondrial transit peptide and a 470-residue mature protein of 50 kD. The derived protein has considerable homology with soybean nodule FLbR-1 (93% identity) and pea (Pisum sativum) leaf mitochondria DLDH (89% identity). The cDNA encoding the mature protein was overexpressed in Escherichia coli. The recombinant enzyme showed Km and kcat values for ferric leghemoglobin that were very similar to those of DLDH. The transcripts of FLbR-2 were more abundant in stems and roots than in nodules and leaves. Immunoblots of nodule fractions revealed that an antibody raised against pea leaf DLDH cross-reacted with recombinant FLbR-2, native FLbR-2 of soybean nodule mitochondria, DLDH from bacteroids, and an unknown protein of approximately 70 kD localized in the nodule cytosol. Immunogold labeling was also observed in the mitochondria, cytosol, and bacteroids of soybean nodules. The similar biochemical, kinetic, and immunological properties, as well as the high amino acid sequence identity and mitochondrial localization, draw us to conclude that FLbR-2 is soybean DLDH.

Targeting of the soybean leghemoglobin to tobacco chloroplasts: effects on aerobic metabolism in transgenic plants

Several attempts have been made to alter the aerobic metabolism of plants, especially those related to the oxygenation or carboxylation of Rubisco. However, designing a more efficient Rubisco protein is rather problematic since its structural manipulation leads frequently to an enhancement of oxygenase activity, which is responsible for photorespiratory losses. In order to reduce oxygen availability inside the chloroplast, a chimeric gene consisting of a soybean leghemoglobin cDNA (lba) ligated to the chloroplast targeting signal sequence of the Rubisco small subunit gene, was introduced and expressed in Nicotiana tabacum. Lb was efficiently imported and correctly processed inside the chloroplasts of transgenic tobacco plants. Furthermore, the level of Lb expression in leaf tissue ranged from 0.01 to 0.1%. Analysis of photosynthesis, starch, sucrose and enzymes involved in aerobic metabolism, revealed that despite the high affinity of Lb for oxygen, no significant difference was observed in relation to the control plants. These results suggest that higher Lb concentrations would be required inside the chloroplasts in order to interfere on aerobic metabolism.

A new class of plant homeobox genes is expressed in specific regions of determinate symbiotic root nodules

A cDNA containing a homeobox sequence was isolated from a soybean nodule-specific expression library. This homeobox cDNA, Ndx (nodulin homeobox), represents a small gene family with at least two members in soybean (Glycine max) and three in Lotus japonicus. One complete 3304 bp Ndx cDNA from L. japonicus encodes a protein, NDX, of 958 amino acids. An unusual type of homeodomain that differs in two of the most conserved amino acid positions in the consensus sequence is located close to the C-terminal and appears to be the only DNA-binding domain. Weak Ndx gene expression in the root increases very shortly after infection with Rhizobium and remains throughout nodule development. In situ hybridizations show cell-specific expression patterns that suggest developmentally separate regions in maturing determinate nodules. Thus in the maturing nodule Ndx and leghemoglobin genes are expressed in a mutually exclusive fashion. The Ndx transcript is also detectable in the young nodule primordium. Ndx expression is not confined to the root nodule since Ndx is also expressed in shoot and root meristems, indicating that the Ndx gene products might also be involved in developmental processes in other plant tissues.

The mini-hemoglobins in neural and body wall tissue of the nemertean worm, Cerebratulus lacteus

Hemoglobin (Hb) occurs in circulating red blood cells, neural tissue, and body wall muscle tissue of the nemertean worm, Cerebratulus lacteus. The neural and body wall tissue each express single major Hb components for which the amino acid sequences have been deduced from cDNA and genomic DNA. These 109-residue globins form the smallest stable Hbs known. The globin genes have three exons and two introns with splice sites in the highly conserved positions of most globin genes. Alignment of the sequences with those of other globins indicates that the A, B, and H helices are about one-half the typical length. Phylogenetic analysis indicates that shortening results in a small tendency of globins to group together regardless of their actual relationships. The neural and body wall Hbs in situ are half-saturated with O2 at 2.9 and 4.1 torr, respectively. The Hill coefficient for the neural Hb in situ, approximately 2.9, suggests that the neural Hb self-associates in the deoxy state at least to tetramers at the 2-3 mM (heme) concentration estimated in the cells. The Hb must dissociate upon oxygenation and dilution because the weight-average molecular mass of the HbO2 in vitro is only about 18 kDa at 2-3 microM heme concentration. Calculations suggest that the Hb can function as an O2 store capable of extending neuronal activity in an anoxic environment for 5-30 min.

Bacterial expression and spectroscopic characterization of soybean leghaemoglobin a

A gene encoding leghaemoglobin a from soybean has been constructed and the soluble recombinant protein expressed in E. coli. The integrity of the recombinant protein has been assessed by a range of spectroscopic techniques. Electrospray mass spectrometry of the protein indicates that the molecular mass of the protein corresponds to the predicted amino acid sequence. Circular dichroism spectra of the ferric derivative and UV-visible spectra of various ferric and ferrous derivatives (pH 6.99, mu = 0.10 M, 25.0 degrees C) are consistent with published data for the wild-type protein. For the ferric derivative, UV-visible (298 and 77 K) and EPR (10 K) spectra indicate the existence of a thermal equilibrium between high- and low-spin forms. Titration of the protein (0.10 M NaCl, mu = 0.10 M, 25.0 degrees C) between pHs 6.68 and 10.35 indicate formation (pKa = 8.3+/-0.03) of a 6-coordinate, hydroxide-bound form of the protein at high pH. All of the above data are consistent with the behaviour of the wild-type protein.

Characterization of recombinant soybean leghemoglobin a and apolar distal histidine mutants

The cDNA for soybean leghemoglobin a (Lba) was cloned from a root nodule cDNA library and expressed in Escherichia coli. The crystal structure of the ferric acetate complex of recombinant wild-type Lba was determined at a resolution of 2.2 A. Rate constants for O2, CO and NO binding to recombinant Lba are identical with those of native soybean Lba. Rate constants for hemin dissociation and auto-oxidation of wild-type Lba were compared with those of sperm whale myoglobin. At 37 degrees C and pH 7, soybean Lba is much less stable than sperm whale myoglobin due both to a fourfold higher rate of auto-oxidation and to a approximately 600-fold lower affinity for hemin. The role of His61(E7) in regulating oxygen binding was examined by site-directed mutagenesis. Replacement of His(E7) with Ala, Val or Leu causes little change in the equilibrium constant for O2 binding to soybean Lba, whereas the same mutations in sperm whale myoglobin cause 50 to 100-fold decreases in K(O2). These results show that, at neutral pH, hydrogen bonding with His(E7) is much less important in regulating O2 binding to the soybean protein. The His(E7) to Phe mutation does cause a significant decrease in K(O2) for Lba, apparently due to steric hindrance of the bound ligand. The rate constants for O2 dissociation from wild-type and native Lba decrease significantly with decreasing pH. In contrast, the O2 dissociation rate constants for mutants with apolar E7 residues are independent of pH, suggesting that hydrogen bonding to the distal histidine residue in the native protein is enhanced under acid conditions. All of these results support the hypothesis that the high affinity of Lba for oxygen and other ligands is determined primarily by enhanced accessibility and reactivity of the heme group.

Cloning of pea storage protein genes

Vicilin and legumin are the major storage proteins of Pisum sativum . Complementary DNAs (cDNAs) have been produced from poly(A) + mRNA isolated from developing seeds and specific storage protein cDNAs cloned into pBR322. The amino acid sequences predicted from the cDNA sequences have been compared with the actual amino acid sequences derived from the purified protein subunits. These comparisons have confirmed that the legumin α and β subunits as initially synthesized are covalently joined together and that a small peptide is subsequently removed by endoproteolysis to give the disulphide linked subunits of the mature seed legumins. Similar comparisons between the predicted amino acid sequence of vicilin cDNA clones and the amino acid sequence determined on the isolated subunits has shown that some of the 50000 M r type subunits are subsequently cleaved to give three subunits as products, i.e. polypeptides of 19000 M r (α), 13500 M r (β) and 12500 M r or 16000 M r if glycosylated (γ). In addition to these three subunits, cleavage at one or other of the two potential cleavage sites, results in a 33000 M r polypeptide (α + β) and a 31000 M r polypeptide tentatively identified as β + γ. The presence of the sequence Lys-Glu-Asn leads to cleavage on the carboxy side of Asn at the β :γ cleavage site whereas the sequence Gly-Leu-Arg does not lead to cleavage. Comparable sequence data for the α: β processing site do not exist. Comparisons of the cDNA and amino acid sequence disclose the presence of a 15 or 16 amino acid residue vicilin leader sequence as well as a 12 amino acid residue C-terminal peptide which is also removed. The codon usage of the messenger RNAs for the storage proteins are similar to those of other plant proteins and differ somewhat from animal messenger RNAs. Complementary DNAs for specific storage proteins when used to probe different restriction enzyme digests of pea genomic DNA reveal the presence of a small number of legumin and vicilin coding sequences (two to five for legumin and three to seven for vicilin) that occur as single copies except for one vicilin sequence present in two to three copies. Genetic mapping experiments using whole plants locate both the main legumin and the vicilin genes on chromosome 7. The main legumin subunits are coded by genes located at a single Mendelian locus Lg-1 located on the short arm of chromosome 7 very close to the rub locus and the vicilin gene is located 16 map units away close to the r locus. Gene libraries prepared with size fractionated partial restriction enzymic digests of pea genomic DNA ligated into both phage λ L47 and phage λ gt wes have led to the isolation of at least three similar but different legumin genomic sequences. Comparison of the λ and cDNA legumin clones suggests the presence of at least one intron in the former. Legumes in general contain two major seed storage protein types, vicilin and legumin (Derbyshire et al. 1976). Seeds of Pisum sativum (L) have significant amounts of both proteins and since a considerable body of knowledge exists about pea physiology and genetics, this species is a good choice for the study of storage protein genes. Peas are also one of the world’s major legume crops. Since the storage proteins are found only in the tissues of the developing seed (Millerd 1975) and then only in significant amounts during the middle and late stages of development, it was suspected from the onset that the genes responsible for the storage protein would belong to the class of developmentally regulated genes, i.e. those that are only switched on in specific tissues over restricted periods of time.

Gene synthesis, high-level expression and assignment of backbone 15N and 13C resonances of soybean leghemoglobin

A synthetic gene for apoleghemoglobin-a from soybean, optimized for expression in Escherichia coli has been designed and synthesized by a recursive polymerase chain reaction technique. The protein has been expressed with high efficiency and a purification protocol has been developed. The holoprotein is readily reconstituted by the addition of heme. 15N- and 15N,13C-labeled samples were produced and backbone 15N and 13C assignments were determined by 2D and 3D NMR spectroscopy. Comparison of the chemical shifts of 13C(alpha) and 13CO with random coil shifts revealed a pattern of secondary structure which correlates well with the one previously derived from homonuclear NMR data and low-resolution X-ray crystallography.

A new hemoglobin gene from soybean: a role for hemoglobin in all plants

We have isolated a new hemoglobin gene from soybean. It is expressed in cotyledons, stems of seedlings, roots, young leaves, and in some cells in the nodules that are associated with the nitrogen-fixing Bradyrhizobium symbiont. This contrasts with the expression of the leghemoglobins, which are active only in the infected cells of the nodules. The deduced protein sequence of the new gene shows only 58% similarity to one of the soybean leghemoglobins, but 85-87% similarity to hemoglobins from the nonlegumes Parasponia, Casuarina, and barley. The pattern of expression and the gene sequence indicate that this new gene is a nonsymbiotic legume hemoglobin. The finding of this gene in legumes and similar genes in other species strengthens our previous suggestion that genomes of all plants contain hemoglobin genes. The specialized leghemoglobin gene family may have arisen from a preexisting nonsymbiotic hemoglobin by gene duplication.

Evolutionary history of introns in a multidomain globin gene

The Artemia hemoglobin contains two subunits that are similar or different chains of nine globin domains. The domains are ancestrally related and are presumed to be derived from copies of an original single-domain parent gene. Since the gene copies have remained in the same environment for several hundred million years they provide an excellent model for the investigation of intron stability. The cDNA for one of the two types of nine-domain subunit (domains T1-T9) has been sequenced. Comparison with the corresponding genomic DNA reveals a total of 17 intradomain introns. Fourteen of the introns are in locations on the protein that are conventional in globins of other species. In eight of the nine domains an intron corresponds to the B helix, amino acid B12, following the second nucleotide (phase 2), and in six domains a G-helix intron is located between G6 and G7 (phase 0). The consistency of this pattern is supportive of the introns having been inherited from a single-domain parent gene. The remaining three introns are in unconventional locations. Two occur in the F helix, either in amino acid F3 (phase 1) in domain T3, or between F2 and F3 (phase 0) in domain T6. The two F introns strengthen an interpretation of intron inheritance since globin F introns are rare, and in domains T3 and T6 they replace rather than supplement the conventional G introns, as though displacement from G to F occurred before that part of the gene became duplicated. It is inferred that one of the F introns subsequently moved by one nucleotide. Similarly, the third unconventional intron location is the G intron in domain T4 which is in G6, phase 2, one nucleotide earlier than the other G introns. Domain T4 is also unusual in lacking a B intron. The pattern of introns in the Artemia globin gene supports a concept of general positional stability but the exceptions, where introns have moved out of reading frame, or have moved by several codons, or have been deleted, suggest that intron displacements can occur after inheritance from an ancient source.

Gene competition and the possible evolutionary role of tumours

The evolutionary role of tumours might consist of providing the conditions for the expression of evolutionary new genes and thus in providing the material for the origin of new cell types. To approach this concept the principle of gene competition is essential. With an increase in gene number in the genomes of the evolving multicellular organisms the enforcement of gene competition should take place. Therefore, the pre-existing cell types possess limited possibilities for the expression of evolutionary new genes. Like evolutionary new genes originated from extra copies (duplicates) of old genes, evolutionary new cell types had to originate from extra cells which were not functionally necessary to the organism. Tumours could have supplied the evolving multicellular organisms with extra cells for the expression of originating evolutionary new genes. Of course, on the basis of this proposal only tumours at the earlier stages of progression are considered to be meaningful, or some kind of tumour-like processes, but not malignant tumours at late stages of progression. The evolutionary new genes originate in the DNA of germ line cells but not in DNA of tumour cells. Until the moment of their expression in the tumour cells these genes could stay silent. After the expression of these genes tumour cells should acquire the function in the organism, differentiate and lose their previous autonomy. The organisms with a new cell type should then be selected against their fitness and competitive abilities.

gsa1 is a universal tetrapyrrole synthesis gene in soybean and is regulated by a GAGA element

Expression of plant tetrapyrroles is high in photosynthetic tissues and in legume root nodules in the form of chlorophyll and heme, respectively. The universal tetrapyrrole precursor delta-aminolevulinic acid (ALA) is synthesized from glutamate 1-semialdehyde (GSA) by GSA aminotransferase in plants, which is encoded by gsa. Immunoblot analysis showed that GSA aminotransferase was expressed in soybean leaves and nodules, but not in roots, and that protein correlated with enzyme activity. These observations indicate that GSA aminotransferase expression is controlled in tetrapyrrole formation and argue against significant activity of an enzyme other than the well described aminotransferase for GSA-dependent ALA formation. gas mRNA and protein were induced in soybean nodules, and their activation was temporally intermediate between those of the respective early and late genes endo2 and lb. A GSA aminotransferase gene, designated gsa1, was isolated and appears to be one of two gsa genes in the soybean genome. gsa1 mRNA accumulated to high levels in leaves and nodules, but not in uninfected roots as discerned with a gsa1-specific probe. Message levels were higher in leaves from etiolated plantlets than in mature plants, and expression in the former was slightly elevated by light. The expression pattern of gsa1 mRNA was qualitatively similar to that of total gsa. The data strongly suggest that gsa1 is a universal tetrapyrrole synthesis gene and that a gsa gene specific for a tissue, tetrapyrrole, or light condition is unlikely. The gsa1 promoter contained a genetic element found in numerous Drosophila melanogaster genes; the so-called GAGA element displayed single-stranded character in vitro and formed a complex with nuclear factors from nodules and leaves but not from roots. From these observations we infer that the GAGA element is involved in the transcriptional control of gsa1.

1H resonance assignments and secondary structure of the carbon monoxide complex of soybean leghemoglobin determined by homonuclear two-dimensional and three-dimensional NMR spectroscopy

Homonuclear two-dimensional and three-dimensional 1H-NMR spectroscopy has been utilized to study the 15.9-kDa protein soybean leghemoglobin. NMR experiments were performed on the diamagnetic carbon monoxide complex at two temperatures and two pH values. Sequence-specific assignments have been made for 94% of the backbone and approximately 70% of the expected side-chain resonances. The secondary structure of leghemoglobin in solution has been determined on the basis of NOE connectivity patterns, hydrogen exchange and chemical-shift analyses. Leghemoglobin consists of seven helices and, unlike mammalian myoglobins, is missing the D helix. Instead an extended loop, the CE loop, is observed which might have importance for ligand entry into and exit from the protein interior. The hydrogen exchange behavior for the F helix and at the beginning of the A helix suggests different dynamic stability compared to other helical regions in leghemoglobin. Population of a second protein conformation, in which there is perturbation at the A-G-H helix interface, is observed at low pH.

Adventitious variability? The amino acid sequences of nonvertebrate globins

1. The more than 140 amino acid sequences of non-vertebrate hemoglobins (Hbs) and myoglobins (Mbs) that are known at present, can be divided into several distinct groups: (1) single-chain globins, containing one heme-binding domain; (2) truncated, single-chain, one-domain globins; (3) chimeric, one-domain globins; (4) chimeric, two-domain globins; and (5) chimeric multi-domain globins. 2. The crystal structures of eight nonvertebrate Hbs and Mbs are known, all of them monomeric, one-domain globin chains. Although these molecules represent plants, prokaryotes and several metazoan groups, and although the inter-subunit interactions in the dimeric and tetrameric molecules differ from the ones observed in vertebrate Hbs, the secondary structures of all seven one-domain globins retain the characteristic vertebrate "myoglobin fold". No crystal structures of globins representing the other four groups have been determined. 3. Furthermore, a number of the one-, two- and multi-domain globin chains participate in a broad variety of quaternary structures, ranging from homo- and heterodimers to highly complex, multisubunit aggregates with M(r) > 3000 kDa (S. N. Vinogradov, Comp. Biochem. Physiol. 82B, 1-15, 1985). 4. (1) The single-chain, single-domain globins are comparable in size to the vertebrate globins and exhibit the widest distribution. (A) Intracellular Hbs include: (i) the monomeric and polymeric Hbs of the polychaete Glycera; (ii) the tetrameric Hb of the echiuran Urechis; (iii) the dimeric Hbs of echinoderms such as Paracaudina and Caudina; and (iv) the dimeric and tetrameric Hbs of molluscs, the bivalves Scapharca, Anadara, Barbatia and Calyptogena. (B) Extracellular Hbs include: (i) the multiple monomeric and dimeric Hbs of the larva of the insect Chironomus; (ii) the Hbs of nematodes such as Trichostrongylus and Caenorhabditis; (iii) the globin chains forming tetramers and dodecamers and comprising approximately 2/3 of the giant (approximately 3600 kDa), hexagonal bilayer (HBL) Hbs of annelids, e.g. the oligochaete Lumbricus and the polychaete Tylorrhynchus and of the vestimentiferan Lamellibrachia; and (iv) the globin chains comprising the ca 400 kDa Hbs of Lamellibrachia and the pogonophoran Oligobrachia. (C) Cytoplasmic Hbs include: (i) the Mbs of molluscs, the gastropods Aplysia, Bursatella, Cerithedea, Nassa and Dolabella and the chiton Liolophura; (ii) the three Hb of the symbiont-harboring bivalve Lucina; (iii) the dimeric Hb of the bacterium Vitreoscilla; and (iv) plant Hbs, including the Hbs of symbiont-containing legumes (Lgbs), the Hbs of symbiont-containing non-leguminous plants and the Hbs in the roots of symbiont-free plants.(ABSTRACT TRUNCATED AT 400 WORDS)

Isolation and characterization of novel nodulin cDNAs representing genes expressed at early stages of soybean nodule development

We took advantage of a subtractive hybridization procedure to isolate a set of cDNA clones of nodule-specific genes (nodulin genes) from developing soybean root nodules. Single-stranded 32P-labelled cDNA synthesized from nodule poly(A)+ RNA was hybridized with a large excess of uninfected root poly(A)+ RNA. Unhybridized cDNA was selected and used to screen nodule cDNA libraries. By this procedure we isolated several novel nodulin cDNA clones together with most of the nodulin cDNAs previously described. Four novel nodulin genes, which were expressed long before the onset of nitrogen fixation, were further characterized. GmN#36 and GmN#93 transcripts appeared in the roots less than 3 days after sowing and inoculation with Bradyrhizobium, but GmN#36 transcripts were also detected at very low levels in the stems of uninfected plants. Transcripts of GmN#315 and GmN#70 first appeared at 6-7 days, just before nodule emergence. Amino acid sequences of the predicted products of GmN#36, GmN#93 and GmN#70 exhibited no significant homology to proteins identified so far. The GmN#315 encoded protein has a limited but significant homology to some plant cyanins, suggesting that it is a metal-binding glycoprotein. In situ hybridization studies revealed that GmN#36 transcripts first appeared in the pericycle cells of the root stele near the infected site. During nodule emergence they were found in a few cell layers surrounding the vascular strands connecting the nodule meristem with the root stele, and in mature nodules they were present specifically in the pericycle cells in vascular bundles. These observations led us to hypothesize that GmN#36 gene products play a role in the transport and/or degradation of photosynthate. On the other hand, GmN#93 transcripts first appeared in the primary nodule meristem just below the root epidermis. In mature nodules they were only present in the infected cells.

A protein alignment scoring system sensitive at all evolutionary distances

Protein sequence alignments generally are constructed with the aid of a "substitution matrix" that specifies a score for aligning each pair of amino acids. Assuming a simple random protein model, it can be shown that any such matrix, when used for evaluating variable-length local alignments, is implicitly a "log-odds" matrix, with a specific probability distribution for amino acid pairs to which it is uniquely tailored. Given a model of protein evolution from which such distributions may be derived, a substitution matrix adapted to detecting relationships at any chosen evolutionary distance can be constructed. Because in a database search it generally is not known a priori what evolutionary distances will characterize the similarities found, it is necessary to employ an appropriate range of matrices in order not to overlook potential homologies. This paper formalizes this concept by defining a scoring system that is sensitive at all detectable evolutionary distances. The statistical behavior of this scoring system is analyzed, and it is shown that for a typical protein database search, estimating the originally unknown evolutionary distance appropriate to each alignment costs slightly over two bits of information, or somewhat less than a factor of five in statistical significance. A much greater cost may be incurred, however, if only a single substitution matrix, corresponding to the wrong evolutionary distance, is employed.

Organization of non-vertebrate globin genes

The organization of non-vertebrate globin genes exhibits substantially more variability than the three-exon, two-intron structure of the vertebrate globin genes. (1) The structures of genes of the single-domain globin chains of the annelid Lumbricus and the mollusc Anadara, and the globin gene coding for the two-domain chains of the clam Barbatia, are similar to the vertebrate plan. (2) Genes for single-domain chains exist in bacteria and protozoa. Although the globin gene is highly expressed in the bacterium Vitreoscilla, the putative globin gene hmp in E. coli, which codes for a chimeric protein whose N-terminal moiety of 139 residues contains 67 residues identical to the Vitreoscilla globin, may be either unexpressed or expressed at very low levels, despite the presence of normal regulatory sequences. The DNA sequence of the globin gene of the protozoan Paramecium, determined recently by Yamauchi and collaborators, appears to consist of two exons separated by a short intron. (3) Among the lower eukaryotes, the yeasts Saccharomyces and Candida have chimeric proteins consisting of N-terminal globin and C-terminal flavoprotein moieties of about the same size. The structure of the gene for the chimeric protein of Saccharomyces exhibits no introns. According to Riggs, the presence of chimeric proteins in E. coli and other prokaryotes, such as Alcaligenes and Rhizobium, as well as in yeasts, suggests a previously unrecognized evolutionary pathway for hemoglobin, namely that of a multipurpose heme-binding domain attached to a variety of unrelated proteins with diverse functions. (4) The published globin gene sequences of the insect larva Chironomus have an intron-less structure and are present as clusters of multiple copies; the expression of the globin genes is tissue and developmental stage-specific. Furthermore, the expression of many of these genes has not yet been demonstrated despite the presence of apparently normal regulatory sequences in the two flanking regions. Unexpectedly, Bergtrom and collaborators have recently shown that at least three Ctt globin II beta genes contain putative introns. (5) Pohajdak and collaborators have found a seven-exon and six-intron structure for the globin gene of the nematode Pseudoterranova which codes for a two-domain globin chain. Although the second and fourth introns of the N-terminal domain correspond to the two introns found in vertebrate globin genes, the position of the third intron is close to that of the central intron in plant hemoglobins.(ABSTRACT TRUNCATED AT 400 WORDS)

The unique structure of the Paramecium caudatum hemoglobin gene: the presence of one intron in the middle of the coding region

The gene encoding hemoglobin (Hb) in the ciliated protist, Paramecium caudatum, has been cloned and sequenced. A single Hb locus was detected on an isolated genomic fragment with a size of approx. 15 kbp. This gene contained 443 bp. The 5' transcriptional regulatory region contained TATA box- and CAAT box-like sequences which resemble the structure of the promoter region in higher eukaryotic genes. The amino acid sequence deduced from the gene agreed precisely with that of the major Hb component. It was an unusual structure, much smaller than Hbs from many other organisms. Furthermore, all of the untranslated regions in this gene were also small. Particularly, one intervening sequence (intron) being only 23 bp was shorter than any other introns reported for eukaryotic genes encoding protein. The position of the intron in the P. caudatum Hb gene corresponded closely to that of the second intron which had been reported only for plant Hb genes. Possible routes for the evolution of Hb genes were discussed.

Unexpected intron location in non-vertebrate globin genes

The Caenorhabditis elegans and Artemia T4 globin sequences are highly homologous with other invertebrate globins. The intron/exon patterns of their genes display a single intron in the E and G helices respectively. Precoding introns in multirepeat globins are inserted in homologous positions. Comparison of the intron/exon patterns in the known globin gene sequences demonstrates that they are more diverse than first expected but nevertheless can be derived from an ancestral pattern having 3 introns and 4 exons.

A single copy gene for chicken chromosomal protein HMG-14b has evolutionarily conserved features, has lost one of its introns and codes for a rapidly evolving protein

The evolutionary origins and common features of the genes coding for the HMG-14/-17 family of chromosomal proteins have been studied by isolating and sequencing the chicken HMG-14b gene, the true homolog of the human and calf HMG-14 gene. Comparison of the structure of this gene to that of the human HMG-14 gene and to the human and chicken HMG-17 genes indicates that the HMG-14 and HMG-17 genes evolved from a common ancestor. We postulate that the ancestral gene consisted of six exons. In all genes the first exon codes for the entire 5' untranslated region and for the first four amino acids, which are invariant among all the known members of the HMG-14/-17 protein family. The last exon codes for ten to 16 amino acids and for the entire 3' untranslated region, which, for each gene, constitutes over 70% of the transcript. The DNA-binding domain of the proteins is encoded by two distinct exons. The genes are characterized by 5' regions that are highly enriched in G + C residues and have features characteristic of "housekeeping" genes. The HMG-17 genes are distinct from the HMG-14 in that the 5' regulatory region of the former has two TATA boxes while the HMG-14 genes have no such regulatory element. The chicken HMG-14b gene is a single-copy gene and produces a unique transcript. In this gene, exons II and III are fused and intron 2 is missing. The fusion of the two exons produced a codon for valine in a position that, among all HMG-14/-17 proteins, is unique to HMG-14b. The possible consequences of a valine insertion at the N-terminal end of the DNA-binding domains are discussed. The HMG-14 proteins evolve significantly faster than HMG-17, suggesting that the proteins are subject to different evolutionary pressure. However, certain amino acids are conserved among all the known members of the HMG-14/-17 protein family, suggesting that they are part of the functional domain of this family of chromosomal proteins.

Cloning and sequence analysis of the genomic DNA fragment encoding oryzacystatin

A genomic DNA clone encoding oryzacystatin (Oc), a cysteine proteinase inhibitor (cystatin) of rice, was isolated from a lambda EMBL3 phage library constructed with Sau3AI partial digests of rice chromosomal DNA, by screening with an oc cDNA as a probe. The restriction map of the isolated DNA fragment was consistent with the pattern of the genomic Southern-blot analysis using a cDNA probe, and consequently, the gene is considered to be a single-copy gene. The oc gene is about 1.4 kb long and composed of three exons and two introns. The first intron (336 bp) intervenes between Ala-38 and Asp-39. The second intron (372 bp) exists in the 3'-noncoding region at the G residue next to the stop codon. S1 nuclease mapping showed the major transcription start point (tsp) at A, 104 bp upstream from the start codon (ATG). Typical CAT and TATA box sequences were found in the 5'-upstream region of the tsp. The nucleotide sequences around the TATA box, the tsp, the start codon, and the stop codon essentially matched the consensus sequences of other higher plant genes. The intron boundaries of the oc gene were quite different from those of the human kininogen-encoding gene and the human salivary cystatin (cystatin S)-encoding gene.

The 5' splice site: phylogenetic evolution and variable geometry of association with U1RNA

The 5' splice site sequences of 3294 introns from various organisms (1-672) were analyzed in order to determine the rules governing evolution of this sequence, which may shed light on the mechanism of cleavage at the exon-intron junction. The data indicate that, currently, in all organisms, a common sequence 1GUAAG6U and its derivatives are used as well as an additional sequence and its derivatives, which differ in metazoa (G/1GUgAG6U), lower eucaryotes (1GUAxG6U) and higher plants (AG/1GU3A). They all partly resemble the prototype sequence AG/1GUAAG6U whose 8 contigous nucleotides are complementary to the nucleotides 4-11 of U1RNA, which are perfectly conserved in the course of phylogenetic evolution. Detailed examination of the data shows that U1RNA can recognize different parts of 5' splice sites. As a rule, either prototype nucleotides at position -2 and -1 or at positions 4, 5 or 6 or at positions 3-4 are dispensable provided that the stability of the U1RNA-5' splice site hybrid is conserved. On the basis of frequency of sequences, the optimal size of the hybridizable region is 5-7 nucleotides. Thus, the cleavage at the exon-intron junction seems to imply, first, that the 5' splice site is recognized by U1RNA according to a "variable geometry" program; second, that the precise cleavage site is determined by the conserved sequence of U1RNA since it occurs exactly opposite to the junction between nucleotides C9 and C10 of U1RNA. The variable geometry of the U1RNA-5' splice site association provides flexibility to the system and allows diversification in the course of phylogenetic evolution.

Characterization of a pollen-specific cDNA clone from Zea mays and its expression

A pollen-specific cDNA clone, Zmc13, has been isolated from a cDNA library constructed to poly(A) RNA from mature maize pollen. The cDNA as shown by primer extension analysis is a full-length copy of the mRNA. The cDNA has been sequenced and is 929 nucleotides in length plus a 47-nucleotide poly(A) tail. Putative polyadenylation signals are identifiable in the 3'-nontranslated region. The mRNA codes for a predicted polypeptide containing 170 amino acid residues and with a molecular mass of 18.3 kilodaltons. The hydropathy profile suggests a possible signal sequence on the amino terminus. A comparison of the nucleotide and deduced amino acid sequence with sequences in data banks has not shown homology to known molecules. In situ hybridizations using RNA probes show that the mRNA is located in the cytoplasm of the vegetative cell of the pollen grain and after germination is distributed throughout the pollen tube cytoplasm.

NMR studies of the conformations of leghemoglobins from soybean and lupin

Phase-sensitive two-dimensional NMR methods have been used to obtain extensive proton resonance assignments for the carbon monoxide complexes of lupin leghemoglobins I and II and soybean leghemoglobin a. The assigned resonances provide information on the solution conformations of the proteins, particularly in the vicinity of the heme. The structure of the CO complex of lupin leghemoglobin II in solution is compared with the X-ray crystal structure of the cyanide complex by comparison of observed and calculated ring current shifts. The structures are generally very similar but significant differences are observed for the ligand contact residues, Phe30, His63 and Val67, and for the proximal His97 ligand. Certain residues are disordered and adopt two interconverting conformations in lupin leghemoglobin II in solution. The proximal heme pocket structure is closely conserved in the lupin leghemoglobins I and II but small differences in conformation in the distal heme pocket are apparent. Larger conformational differences are observed when comparisons are made with the CO complex of soybean leghemoglobin. Altered protein-heme packing is indicated on the proximal side of the heme and some conformational differences are evident in the distal heme pocket. The small conformational differences between the three leghemoglobins probably contribute to the known differences in their O2 and CO association and dissociation kinetics. The heme pocket conformations of the three leghemoglobins are more closely related to each other than to sperm whale myoglobin. The most notable differences between the leghemoglobins and myoglobin are: (a) reduced steric crowding of the ligand binding site in the leghemoglobins, (b) different orientations of the distal histidine, and (c) small but significant differences in proximal histidine coordination geometry. These changes probably contribute to the large differences in ligand binding kinetics between the leghemoglobins and myoglobin.

Identification of two groups of leghemoglobin genes in alfalfa (Medicago sativa) and a study of their expression during root nodule development

Differential screening of an alfalfa root nodule cDNA library with either root or nodule mRNA resulted in the isolation of two groups of leghemoglobin cDNA which differ significantly in sequence. Analysis of one member of each group revealed a divergence within the coding region of 15% at the nucleotide level and 14% at the amino acid level. The 3' non-coding sequences are 25% divergent but are highly conserved over a stretch of 54 nucleotides which contains two sequence motifs common to leghemoglobin genes from other plant species. Southern blotting analysis with exon-specific probes has shown that there are approximately twice as many leghemoglobin gene copies in the alfalfa genome corresponding to one type of cDNA as compared with the other. Using the same criterium of DNA sequence relatedness these two distinct groups of leghemoglobin genes have also been identified in the genomes of the diploid annual Medicago truncatula and the closely related genus, Melilotus. Transcripts corresponding to both groups of leghemoglobin genes are first detected in alfalfa nodules 9-10 days after Rhizobium inoculation. Thereafter, mRNA levels increase rapidly and synchronously, reaching a maximum approximately 2 days later. There is a 2-3 fold difference in the steady-state levels of the two mRNA populations and this is maintained throughout the subsequent two weeks of nodule growth. The absence of any detectable transcription during the early stages of nodule development and the apparent co-ordinate expression of leghemoglobin genes in alfalfa contrasts with the situation in soybean and suggests that important differences in leghemoglobin gene regulation exist between these two distantly related legume species.

Cloning, characterization and expression of the bacterial globin gene from Vitreoscilla in Escherichia coli

The genomic locus responsible for production of the globin portion of Vitreoscilla hemoglobin (VtHb), the only well-characterized bacterial hemoglobin (Hb), has been cloned and expressed in Escherichia coli. A 17-mer oligodeoxynucleotide, corresponding to a region of the VtHb amino acid sequence was used as a hybridization probe to screen a Vitreoscilla genomic library constructed in broad-host-range cosmid vector pVK102. E. coli, carrying recombinant pVK102:H5 which contained a 16.5-kb insert of Vitreoscilla genomic DNA, produced three to four times more Hb than Vitreoscilla. Restriction mapping and subcloning revealed that the globin-coding gene (vgb) was completely localized on a 1.4-kb HindIII-SalI fragment of the 16.5-kb insert. Production of VtHb still occurred when this 1.4-kb fragment was cloned in plasmids pUC8 and pUC9 in opposite orientations, suggesting the presence of a Vitreoscilla promoter on this fragment. A single copy of this gene on the chromosome was indicated by Southern-blot analysis, and a 450-500-nt RNA transcript specific for the globin gene was detected after Northern hybridization. A partially purified Hb preparation from E. coli harboring the recombinant plasmid had identical spectral properties and subunit molecular size as authentic VtHb. The Hb in respiring cells of E. coli was in the physiologically functional oxyHb form.

Primary structure and promoter analysis of leghemoglobin genes of the stem-nodulated tropical legume Sesbania rostrata: conserved coding sequences, cis-elements and trans-acting factors

The primary structure of a leghemoglobin (lb) gene from the stem-nodulated, tropical legume Sesbania rostrata and two lb gene promoter regions was analysed. The S. rostrata lb gene structure and Lb amino acid composition were found to be highly conserved with previously described lb genes and Lb proteins. Distinct DNA elements were identified in the S. rostrata lb promoter regions, which share a high degree of homology with cis-active regulatory elements found in the soybean (Glycine max) lbc3 promoter. One conserved DNA element was found to interact specifically with an apparently universal, trans-acting factor present in nuclear extracts of nodules. These results suggest a conserved mechanism for nodule specific induction of lb genes in leguminous plants.

Plant intron sequences: evidence for distinct groups of introns

In vivo and in vitro RNA splicing experiments have demonstrated that the intron splicing machineries are not interchangeable in all organisms. These differences have prevented the efficient in vivo expression of monocot genes containing introns in dicot plants and the in vitro excision of some plant introns in HeLa cell in vitro splicing extracts. We have analyzed plant introns for sequence differences which potentially account for the functional splicing differences. Three classes of plant introns can be differentiated by the purine or pyrimidine-richness of sequences upstream from the 3' splice site. The frequency of these three types of introns in monocots and dicots varies significantly. The degree of variability in the 5' and 3' intron boundaries is evaluated for each of these classes in monocots and dicots. The 5' splice site consensus sequences developed for the monocot and dicot introns differ in their ability to base pair with conserved nucleotides present at the 5' end of many U1 snRNAs.