Signal perception, differential expression within multigene families and the molecular basis of phenotypic plasticity

Abstract. This Introduction to the Special Issue of Plant, Cell and Environment on 'Sensing the Environment'is concerned with the molecular mechanisms that may link the perception of environmental signals with the evocation of those specific developmental responses that collectively are known as phenotypic plasticity. The significance of phenotypic plasticity at the evolutionary, developmental and ecological levels is outlined, and it is argued that the extent of an individual's adaptability to environmental conditions must be a reflection of the extent and sophistication of the controls over the synthesis and action of specific proteins. Reviewing evidence from a selected range of plant enzymes and regulatory proteins, it is proposed that differential regulation of the expression of members of multigene families may represent the molecular basis of phenotypic plasticity.     

Proline-rich proteins and glycoproteins: expression of salivary gland multigene families

Our recent research interests have focused on a group of unusual proteins and glycoproteins high in proline content, or the so-called proline-rich proteins (PRPs). The PRPs are tissue-specific expressions of salivary gland multigene families. Normally PRPs are not detected or are present in very low amounts in rat, mouse and hamster salivary glands, but these unusual proteins are dramatically induced by treatment with the catecholamine isoproterenol. The structures and organizations of several PRP mRNAs and PRP genes have been determined. The amino acid sequences of all PRPs show 4 distinct regions, namely, a signal peptide, a transition region, a repeat region and a carboxyl-terminal region. Glycoproteins induced by isoproterenol treatment may be N-glycosylated or O-glycosylated. The N-glycosylated glycoprotein GP-158 from rat submandibular glands has a 12 amino acid glycopeptide which repeats possibly 49 times. Proline-rich proteins of the parotid glands of rats and mice are also greatly induced by dietary tannins. The apparent unique occurrence of PRPs in saliva suggests that one biological role is to neutralize the detrimental effects of dietary tannins and other polyphenols. The upstream regions of the mouse and hamster PRP genes contain cyclic AMP-regulated sequences as demonstrated by deletions and transient transfections. The PRP multigene family members of mouse are all located on chromosome 8.     

Chicken nonmuscle myosin heavy chains: differential expression of two mRNAs and evidence for two different polypeptides

Two different mRNAs encoding two different nonmuscle myosin heavy chains (MHCs) of approximately 200 kD have been identified in chicken nonmuscle cells, in agreement with the results of Katsuragawa et al. (Katsuragawa, Y., M. Yanagisawa, A. Inoue, and T. Masaki. 1989. Eur. J. Biochem. 184:611-616). In this paper, we quantitate the content of mRNA encoding the two MHCs in a number of different tissues using RNA blot analysis with two specific oligonucleotide probes. Our results show that the relative content of mRNA encoding MHC-A and MHC-B differs in a tissue-dependent manner. Thus the ratio of mRNA encoding MHC-A versus MHC-B varies from greater than 9:1 in spleen and intestinal epithelial cells, to 6:4 in kidney and 2:8 in brain. The effect of serum on MHC mRNA expression was studied in serum-starved cultures of chick embryo fibroblasts. Serum stimulation results in a threefold increase in the mRNA encoding MHC-A and a threefold decrease in mRNA encoding MHC-B. Using SDS polyacrylamide gels, we have separated two nonmuscle MHC isoforms (198 and 196 kD) that can be distinguished from each other by two-dimensional peptide mapping of chymotryptic digests. We provide preliminary evidence that the MHC-A mRNA encodes the 196-kD polypeptide and that the MHC-B mRNA encodes the 198-kD polypeptide.     

The silkmoth late chorion locus. I. Variation within two paired multigene families

The 140 X 10(3) base late chorion locus of Bombyx mori contains two 15-member multigene families arranged in tightly linked pairs, which are divergently transcribed (the high-cysteine A (HcA) and the high-cysteine B (HcB) families). Previous DNA hybridization experiments have indicated that all members of these gene families contain a complex pattern of shared sequence variation. The sequence analysis in this paper involving all 15 gene pairs allows a comprehensive examination of the nature of this variation. Average sequence homology between gene pairs is: 95% for the protein-encoding regions; 93% for the common 272 base-pair 5' flanking region; 87% for the introns; and 88% for the 3' untranslated regions. Considering the great degree of sequence homology in the coding regions, an unexpectedly high level of variation is found in the deduced protein sequences. Over 50% of the nucleotide substitutions in the protein-encoding regions lead to amino acid replacements, most of which involve a change in charge or effect the secondary structure of the protein. In addition, significant differences in length between the proteins occur in the carboxyl-terminal arm. In both families, the major portion of this arm is composed of Cys-Gly-Gly and Cys-Gly subrepeats forming a (Cys-Gly-Gly)2-(Cys-Gly)2 major repeat. Differences in the number of complete and partial repeats results in deduced protein sequences that contain arms varying from 32 to 54 amino acid residues for members of the HcA family and 14 to 88 residues for the HcB family. The high level of variation in protein composition indicates a lack of strong selective pressure. We suggest the high level of DNA sequence homology maintained by these genes in the coding as well as in the non-coding regions is the result of sequence exchange between family members.     

The profilin multigene family of maize: differential expression of three isoforms

Profilin is a small (12–15 kDa) actin- and phospholipid-binding protein previously known only from studies on animals and lower eukaryotes but recently identified as a birch pollen allergen. Here we have identified and characterized three members of the profilin multigene family from the plant Zea mays . Two cDNAs isolated from a maize pollen library ( ZmPRO 1 and ZmPRO 3) each have a single, large open reading frame encoding a putative polypeptide 131 amino acids long with a predicted molecular weight of approximately 14 kDa. A third maize pollen cDNA ( ZmPRO 2) has two in-frame translation initiation codons. Use of the first ATG would result in a polypeptide 137 amino acids long with a molecular weight of 14.8 kDa. The three maize profilins are highly homologous to each other (>90% nucleotide and amino acid sequence identity) as well as other plant profilins but show far less similarity (30–40% amino acid sequence identity) to animal and lower eukaryote profilins. Multiple sequence alignments indicate that only nine residues are shared by all eukaryotic profilins examined. However, limited comparisons reveal domains in the NH₂ and COOH termini that have a high degree of similarity suggesting functional conservation. The maize gene family size is estimated to contain three to six members based on Southern blot experiments with gene-specific and coding region probes. Northern blot analysis demonstrates that the three maize profilin cDNAs characterized here are utilized in a tissue-specific manner and are anther or pollen specific.     

Evolution of two major chorion multigene families as inferred from cloned cDNA and protein sequences

Complete or partial sequences are reported from six chorion cDNA clones of the silkmoth Antheraea polyphemus. The proteins encoded belong to the two major chorion protein classes, A and B, each of which is encoded by a multigene family. The sequence comparisons define some major features of the families and suggest how these genes may be evolving. Deletions and insertions might be involved in expanding or contracting internally repetitive regions. Sequence divergence is localized, thus defining sequence domains of distinct evolutionary properties and presumably distinct functions.     

Cloning of a type I keratin from goldfish optic nerve: differential expression of keratins during regeneration

We report the cDNA sequence and predicted amino acid sequence of a novel type I keratin, designated as GK50, and show that keratin expression in the goldfish optic nerve is highly complex. The GK50 protein is one of at least three type I keratins expressed in goldfish optic nerve based on both antibody reactivity and blot-binding to the type II keratin ON3. After optic nerve crush in situ hybridization shows a localized increase in GK50 mRNA expression in the crush zone. This is in contrast to ON3 mRNA which shows a localized increase that is limited to the proximal and distal margins of the crush zone, suggesting a diversity of keratin expression in different cell types of the goldfish optic nerve.     

Polyphenol oxidase in potato. A multigene family that exhibits differential expression patterns.

Polyphenol oxidase (PPO) activity in potato (Solanum tuberosum) plants was high in stolons, tubers, roots, and flowers but low in leaves and stems. PPO activity per tuber continued to increase throughout tuber development but was highest on a fresh weight basis in developing tubers. PPO activity was greatest at the tuber exterior, including the skin and cortex tissue 1 to 2 mm beneath the skin. Flowers had high PPO activity throughout development, particularly in the anthers and ovary. Five distinct cDNA clones encoding PPO were isolated from developing tuber RNA. POT32 was the major form expressed in tubers and was found in all parts of the tuber and at all stages of tuber development. It was also expressed in roots but not in photosynthetic tissues. POT33 was expressed in tubers but mainly in the tissue near the skin. POT72 was detected in roots and at low levels in developing tubers. NOR333 was identical with the P2 PPO clone previously isolated from potato leaves (M.D. Hunt, N.T. Eannetta, Y. Haifeng, S.M. Newman, J.C. Steffens [1993] Plant Mol Biol 21: 59-68) and was detected in young leaves and in tissue near the tuber skin but was highly expressed in flowers. The results indicate that PPO is present as a small multigene family in potato and that each gene has a specific temporal and spatial pattern of expression.     

Malaria multigene families: the price of chronicity

In this article, Georges Snounou, William Jarra and Peter Preiser discuss the survival strategy of malaria parasites in the light of a novel mechanism of clonal phenotypic variation recently described for a multigene family of Plasmodium yoelii yoelii. The 235 kDa rhoptry proteins (Py235) encoded by these genes may be involved in the selection of red blood cells for invasion by merozoites. The new mechanism may explain the ability of individual parasites to adapt to natural variations in red blood cell subsets, while ensuring that sufficient merozoites escape immune attack, thus maintaining a chronic infection for extended periods. This counterpoints the antigenic variation exemplified by PfEMP1 proteins (a large family of proteins derived from P. falciparum), which operates at the population level. The possibility of manipulating the expression of functionally similar genes in other Plasmodium species could lead to therapies aimed at reducing clinical severity without compromising the acquisition and maintenance of immunity.     

Transient expression of simple epithelial keratins by mesenchymal cells of regenerating newt limb

Structural proteins of the intermediate filament family are an early indicator of differentiation before organogenesis becomes apparent. Keratin intermediate filaments are characteristically expressed only by epithelial and not by mesenchymal cells. Here we show, using monoclonal antibodies, a transient expression of the keratin pair 8 and 18 in a population of mesenchymal cells in the regenerating newt limb, specifically in the undifferentiated progenitor cells (blastemal cells) which give rise to the new tissues. These keratins are also expressed in cultured limb cells that can differentiate into muscle. In contrast no reactivity with anti-keratin 8 and 18 antibodies was observed in the newt limb bud at an early stage of development, indicating a molecular difference between the developing and regenerating limb. The molecular weights of the newt proteins detected by these antibodies are very similar to those of human keratins 8 and 18, further supporting the immunocytochemical evidence that the newt homologs of these keratins are expressed in blastemal cells. This is the first demonstration of keratin expression in mesenchymal progenitor cells in an adult animal.     

Embryonic simple epithelial keratins 8 and 18: chromosomal location emphasizes difference from other keratin pairs.

The keratins 8 and 18 of simple epithelia differ from stratified epithelial keratins in tissue expression and regulation. To examine the specific properties of human keratin 8, we cloned and sequenced the cDNA from a placental mRNA expression library and defined the optimum state of such clones for expression in bacterial plasmid vectors. Using the polymerase chain reaction we identified and sequenced three introns and located the single active gene for keratin 8, out of a background of 9 to 24 pseudogenes, on chromosome 12. This chromosome contains several genes for type II keratins and also the gene for keratin 18, the type I keratin that is coexpressed with keratin 8. This location of both members of a keratin pair on a single chromosome is thus far unique among the keratin genes; it is consistent with the hypothesis that keratins 8 and 18 may be closer to an ancestral keratin gene than the keratins of more highly differentiated epithelia.     

Genome-wide differential expression of long noncoding RNAs and mRNAs in ovarian follicles of two different chicken breeds

Bashang long-tail chickens are an indigenous breed with dual purpose in China (meat and eggs) but have low egg laying performance. To improve the low egg laying performance, a genome-wide analysis of mRNAs and long noncoding RNAs (lncRNAs) from Bashang long-tail chickens and Hy-Line brown layers was performed. A total of 16,354 mRNAs and 8691 lncRNAs were obtained from ovarian follicles. Between the breeds, 160 mRNAs and 550 lncRNAs were found to be significantly differentially expressed. Integrated network analysis suggested some differentially expressed genes were involved in ovarian follicular development through oocyte meiosis, progesterone-mediated oocyte maturation, and cell cycle. The impact of lncRNAs on cis and trans target genes, indicating some lncRNAs may play important roles in ovarian follicular development. The current results provided a catalog of chicken ovarian follicular lncRNAs and genes for further study to understand their roles in regulation of egg laying performance.     

Tissue specificity and developmental expression of rat osteopontin

Osteopontin is a 44 kd phosphoprotein abundant in bone matrix. We isolated a partial length cDNA for rat osteopontin and used it to examine its tissue specificity, its expression during bone development and its hormonal regulation. Osteopontin mRNA is most abundant in bone but is also found in considerable amounts in kidney. Osteopontin mRNA is regulated by the osteotropic hormones dexamethasone and 1,25(OH)2D3. Estimates of osteopontin mRNA levels indicate that the osteopontin gene is turned on relatively late in calvarial development.