Papain-like and legumain-like proteases in rice: genome-wide identification, comprehensive gene feature characterization and expression analysis

BACKGROUND

Papain-like and legumain-like proteases are proteolytic enzymes which play key roles in plant development, senescence and defense. The activities of proteases in both families could be inhibited by a group of small proteins called cystatin. Cystatin family genes have been well characterized both in tobacco and rice, suggesting their potential roles in seed development. However, their potential targets, papain-like and legumain-like proteases, have not been well characterized in plants, especially in rice, a model plant for cereal biology.

RESULTS

Here, 33 papain-like and 5 legumain-like proteases have been identified in rice genome, respectively. Gene structure, distribution in rice chromosome, and evolutionary relationship to their counterparts in other plants have been well characterized. Comprehensive expression profile analysis revealed that two family genes display divergent expression pattern, which are regulated temporally and spatially during the process of seed development and germination. Our experiments also revealed that the expression of most genes in these two families is sensitively responsive to plant hormones and different abiotic stresses.

CONCLUSIONS

Genome-wide identification and comprehensive gene expression pattern analysis of papain-like and legumain-like proteases in rice suggests their multiple and cooperative roles in seed development and response to environmental variations, which provides several useful cues for further in-depth study.

The stereotyped positioning of the generative cell associated with vacuole dynamics is not required for male gametogenesis in rice pollen

During male gametogenesis in cereals, the generative cell undergoes a positioning process that parallels the dynamics of the central vacuole, which is believed to be associated with generative cell movement in the male gametophyte. However, the impact of the generative cell positioning and the central vacuole dynamics on male gametogenesis has remained poorly understood. Here, we report that OsGCD1 (GAMETE CELLS DEFECTIVE1) dysfunction influenced pollen development and disrupted pollen germination. Loss of function of OsGCD1 altered the central vacuole dynamics and the generative cell was mispositioned. Nevertheless, twin sperm cells were generated normally, indicating that gametogenesis does not rely on positional information as long as a generative cell is produced. The normal vacuole dynamics seems necessary only for pollen maturation and germination. Our findings also indicate that osgcd1 mutation resulted in rice male sterility in which pollen has full cell viability and generated normal gametes, but lacks the potential to germinate.

The suspensor as a model system to study the mechanism of cell fate specification during early embryogenesis

The advances in the suspensor. During early embryogenesis, the proembryo consists of two domains, the embryo proper and the suspensor. Unlike the embryo proper, which has been investigated extensively, research on the suspensor has been limited in past decades. Recent studies have revealed that the suspensor plays an important role in early embryogenesis and the process of suspensor formation and degeneration may provide a unique model for studies on cell division pattern, cell fate determination, and cell death. In this review, we briefly summarize the advances in research on the suspensor, which provide new insight in our understanding of the mechanism of early embryogenesis and show great potential for a unique model for future investigations.

Ribosomal protein NtRPL17 interacts with kinesin-12 family protein NtKRP and functions in the regulation of embryo/seed size and radicle growth

We previously reported that a novel motor protein belonging to the kinesin-12 family, NtKRP, displays critical roles in regulating embryo and seed size establishment. However, it remains unknown exactly how NtKRP contributes to this developmental process. Here, we report that a 60S ribosomal protein NtRPL17 directly interacts with NtKRP. The phenotypes of NtRPL17 RNAi lines show notable embryo and seed size reduction. Structural observations of the NtRPL17-silenced embryos/seeds reveal that the embryo size reduction is due to a decrease in cell number. In these embryos, cell division cycle progression is delayed at the G2/M transition. These phenotypes are similar to that in NtKRP-silenced embryos/seeds, indicating that NtKRP and NtRPL17 function as partners in the same regulatory pathway during seed development and specifically regulate cell cycle progression to control embryo/seed size. This work reveals that NtRPL17, as a widely distributed ribosomal protein, plays a critical role in seed development and provides a new clue in the regulation of seed size. Confirmation of the interaction between NtKRP and NtRPL17 and their co-function in the control of the cell cycle also suggests that the mechanism might be conserved in both plants and animals.

The autonomous cell fate specification of basal cell lineage: the initial round of cell fate specification occurs at the two-celled proembryo stage

In angiosperms, the first zygotic division usually gives rise to two daughter cells with distinct morphologies and developmental fates, which is critical for embryo pattern formation; however, it is still unclear when and how these distinct cell fates are specified, and whether the cell specification is related to cytoplasmic localization or polarity. Here, we demonstrated that when isolated from both maternal tissues and the apical cell, a single basal cell could only develop into a typical suspensor, but never into an embryo in vitro. Morphological, cytological and gene expression analyses confirmed that the resulting suspensor in vitro is highly similar to its undisturbed in vivo counterpart. We also demonstrated that the isolated apical cell could develop into a small globular embryo, both in vivo and in vitro, after artificial dysfunction of the basal cell; however, these growing apical cell lineages could never generate a new suspensor. These findings suggest that the initial round of cell fate specification occurs at the two-celled proembryo stage, and that the basal cell lineage is autonomously specified towards the suspensor, implying a polar distribution of cytoplasmic contents in the zygote. The cell fate transition of the basal cell lineage to the embryo in vivo is actually a conditional cell specification process, depending on the developmental signals from both the apical cell lineage and maternal tissues connected to the basal cell lineage.

[Analysis of early response to the antipsychotic treatment and related factors in acute schizophrenia patients]

Objective: The objective was to assess the relationship between early response and later response to antipsychotics, and the relationship between antipsychotics and early response. Methods: Data were retrospectively analyzed from patients with schizophrenia and they were hospitalized in the Second Affiliated Hospital of Xinxiang Medical College from May, 2013 to September, 2015.The patients were divided into theearly response group (PANSS total score improvement ≥20% at week 2) and early nonresponse group.General information, the use of drug and the Positive and Negative Syndrome Scale (PANSS) on before and 2, 4, 6 weeks after treatment were compared between the two groups.The relation between early response and late response and the effect of drug selection on early response were analyzed by correlation analysis and regression analysis. Results: Relative to early nonresponders, early responders were significantly more likely to have lower PANSS scores (total scores on 2, 4, 6 weeks after treatment 66.2±11.8 vs 84.5±10.9, 55.9±13.2 vs 70.9±13.7, 48.9±13.1 vs 60.6±14.9, all P<0.05) and higher PANSS scores improvement at 2, 4, 6 weeks after treatment (total scores improvement on 2, 4, 6 weeks after treatment (37±14)% vs (9±7)%, (56±19)% vs (32±18)%, (68±20)% vs (49±21)%, all P<0.05). The correlation coefficient between PANSS total score improvement at week 2 and at week 4, 6 were 0.730 and 0.541, respectively (all P<0.05). Olanzapine had more PANSS total score improvement than aripiprazole, quetiapine and ziprasidone (2 weeks after treatment (29±19)% vs (19±16)%, (18±15)%, (17±15)%, 4 weeks after treatment (51±21)% vs (37±25)%, (39±18)%, (37±22)%, all P<0.05). The protective factor for early response was olanzapine (P<0.05). Conclusions: Early responders are associated with faster and greater improvement in symptoms, the type of antipsychotic has impacts on early response, early non-responders can benefit from adjustment of treatment.

OsGCD1 is essential for rice fertility and required for embryo dorsal-ventral pattern formation and endosperm development

Rice fertility is critical for rice reproduction and is thus a focus of interest. Most studies have addressed male sterility and its relation to rice production. The mechanisms of regulation of embryogenesis and endosperm development are essential for rice reproduction, but remain largely unknown. Here, we report a functional analysis of the rice gene OsGCD1, which encodes a highly conserved homolog of Arabidopsis GCD1 (GAMETE CELLS DEFECTIVE1). OsGCD1 mutants were generated using the CRISPR/Cas9 system and subjected to functional analysis. The homozygote mutants cannot be obtained, whereas heterozygotes showed altered phenotypes. In the majority of aborted seeds, the endosperm nucleus divided a limited number of times. The free nuclei were distributed only at the micropylar end of embryo sacs, and their oriented positioning was blocked. In addition, aleurone differentiation was interrupted. The embryo developed slowly, and pattern formation, particularly the dorsal-ventral pattern and symmetry establishment, of embryos was disturbed. Thus, the embryos showed various morphological and structural dysplasias. Our findings reveal that OsGCD1 is essential for rice fertility and is required for dorsal-ventral pattern formation and endosperm free nucleus positioning, suggesting a critical role in sexual reproduction of both monocotyledon and dicotyledon plants.

Identification of genes related to floral organ development in pak choi by expression profiling

Pak choi is a highly nutritious vegetable that is widely grown in China, Southeast Asia, and other parts of the world. Because it reproduces by seed, it is very important to understand the mechanism of floral organ development. Therefore, using the Chinese cabbage genome as a reference, this study analyzed the expression profiles of shoot apex genes at flower bud differentiation stages 1 and 5, in order to identify genes related to floral organ development. The results showed that the proportion of mapped genes was high, with 84.25 and 83.80% of clean reads from the two sample saligned to the reference genome, respectively. A total of 525 differentially expressed genes (DEGs) were identified, 224 of which were upregulated and 301 were downregulated. The expression levels of genes homologous to Chinese cabbage flowering genes were also analyzed at stages 1 and 5; the expression levels of Bra012997 (ap1), Bra000393 (SOC1), and Bra004928 (SOC1) were significantly upregulated at stage 5, suggesting that these three genes positively regulate floral development in pak choi. DEGs involved in floral organ development were analyzed with homologous genes from Arabidopsis thaliana; the homologous genes Bra029281 (AGL42), Bra026577 (ARPN), Bra022954 (SPL3), Bra029293 (ARF2), Bra007978 (AtRLP12), Bra033221 (SPL8), Bra008037 (LOX4), Bra001598 (IAA19), Bra003892 (PATL1), Bra038778 (AT4G21323), Bra025315 (KLCR2), and Bra013906 (DTX35) are directly related to floral organ development in Arabidopsis, suggesting that these genes have corresponding functions during flower organ development in pak choi, and could be candidates for further genetic research. These results provide a foundation for research on the molecular mechanism of flower organ development in pak choi and other Brassica rapa vegetables.

Does Early Embryogenesis in Eudicots and Monocots Involve the Same Mechanism and Molecular Players?

A comparison of eudicot and monocot model plants explores recent advances and open questions on gene regulatory networks during zygote development, parental influences on early embryogenesis, zygotic genome activation, and cell fate determination.

NtDRP is necessary for accurate zygotic division orientation and differentiation of basal cell lineage toward suspensor formation

Plant embryogenesis begins with an asymmetric division of the zygote, producing apical and basal cells with distinct cell fates. The asymmetric zygote division is thought to be critical for embryo pattern formation; however, the molecular mechanisms regulating this process, especially maintaining the accurate position and proper orientation of cell division plane, remain poorly understood. Here, we report that a dynamin-related protein in Nicotiana tabacum, NtDRP, plays a critical role in maintaining orientation of zygotic division plane. Down-regulation of NtDRP caused zygotic cell division to occur in different, incorrect orientations and resulted in disruption of suspensor formation, and even development of twin embryos. The basal cell lineage totally integrated with the apical cell lineage into an embryo-like structure, suggesting that NtDRP is essential to accurate zygotic division orientation and differentiation of basal cell lineage toward suspensor formation. We also reveal that NtDRP plays its role by modulating microtubule spatial organization and spindle orientation during early embryogenesis. Thus, we revealed that NtDRP is involved in orientation of the asymmetric zygotic division and differentiation of distinct suspensor and embryo domains, as well as subsequent embryo pattern formation.

NtKRP, a kinesin-12 protein, regulates embryo/seed size and seed germination via involving in cell cycle progression at the G2/M transition

Kinesins comprise a superfamily of microtubule-based motor proteins involved in essential processes in plant development, but few kinesins have been functionally identified during seed development. Especially, few kinesins that regulate cell division during embryogenesis have been identified. Here we report the functional characterization of NtKRP, a motor protein of the kinesin-12 family. NtKRP is predominantly expressed in embryos and embryonic roots. NtKRP RNAi lines displayed reductions in cell numbers in the meristematic zone, in embryonic root length, and in mature embryo and seed sizes. Furthermore, we also show that CDKA;1 binds to NtKRP at the consensus phosphorylation sites and that the decreased cell numbers in NtKRP-silenced embryos are due to a delay in cell division cycle at the G2/M transition. In addition, binding between the cargo-binding tail domain of NtKRP and CDKA; 1 was also determined. Our results reveal a novel molecular pathway that regulates embryo/seed development and critical role of kinesin in temporal and spatial regulation of a specific issue of embryo developmental.

Asymmetric zygote division: A mystery starting point of embryogenesis

In angiosperm, asymmetric zygote division is critical for embryogenesis. The molecular mechanism underlying this process has gained a great attention recently. Some players involve in the control of both accurate position and correct orientation of zygote division plane have been found, which provide useful clues for the extensive investigations. It is getting clear that both internal and external factors are involved in this complex regulatory mechanism and the asymmetric zygote division seems with great impact in cell fate determination and embryo pattern formation.

Autophagy in sexual plant reproduction as an emerging field

Autophagy is an evolutionary conserved system for clearing and recycling cellular components. Critical roles of autophagy in the responses of plant to different environmental stresses have been revealed during past decades. However, little is known about the role of autophagy in plant developmental processes, especially in the processes of sexual plant reproduction. Here, we briefly discuss recent advances in the emerging field and wish to bring some potential research directions into attention. Possible divergence of molecular mechanism of autophagy in respect to the current debatable view is also discussed.

Initiation of programmed cell death in the suspensor is predominantly regulated maternally in a tobacco hybrid

Maternal gene products deposited in the egg regulate early embryogenesis before activation of the embryonic genome in animals. While in higher plants, it is believed that genes of parental origin contribute to early embryogenesis. However, little is known regarding the particular processes in which genes of parental origin are involved during early embryogenesis. Previously, we found that the initiation of programmed cell death (PCD) in the suspensor of the embryo is regulated by the cystatin, NtCYS. Here, we confirmed that both parental transcripts contribute to PCD, but the relative expression level of the maternal NtCYS allele was much higher than that of the paternal allele in early embryos of tobacco interspecific hybrids. The expression level of the maternal NtCYS allele was decreased markedly, which was necessary for the initiation of PCD, while the paternal allele didn't change. Interestingly, the pattern of PCD in the hybrid suspensor and the morphology of the hybrid suspensor were similar to those of the maternal parent. Our results suggest that NtCYS-mediated PCD initiation in the hybrid suspensor is likely controlled in a maternal dominant manner. This finding represents an example of the involvement of parental transcripts in a specific developmental event during early embryogenesis.

Detection and study of plasma D-dimer change in patients with acute exacerbation of chronic obstructive pulmonary disease

The purpose of this study was to observe the change in plasma D-dimer of patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD). The patients were divided into three groups, i.e., AECOPD group, stable COPD group (COPD kept stable after treatment) and a healthy control group. The content of plasma fibrinogen (FIB) and D-dimer of all research subjects was detected and the difference between groups was analyzed. Moreover, pulmonary functions of patients in the AECOPD group and the stable COPD group, including forced expiratory volume in 1 second (FEV1%) and forced vital capacity rate of 1 second (FEV1/FVC), and blood gas (oxygen partial pressure (PO₂) and partial pressure of carbon dioxide (PaCO₂), were detected; and the differences between the two groups and the possible correlation were analyzed. Compared to the COPD stable group and the control group, the AECOPD group had a statistically significant higher content of plasma FIB and D-dimer (p less than 0.05); the content of plasma FIB and D-dimer of the COPD stable group was much higher than that of the healthy control group, but the difference had no statistical significance (p > 0.05); the content of D-dimer of AECOPD patients was in a negative correlation with FEV1 and PO₂ (p smaller than 0.05) and in a positive correlation with PCO₂ (p smaller than 0.05). It can be concluded that D-dimer is correlated to the severity of AECOPD; hence, it can be used as an evaluation index for the severity of AECOPD.

Direct evidence that suspensor cells have embryogenic potential that is suppressed by the embryo proper during normal embryogenesis

The suspensor is a temporary supporting structure of proembryos. It has been proposed that suspensor cells also possess embryogenic potential, which is suppressed by the embryo as an effect of the embryo-suspensor interaction. However, data to support this hypothesis are not yet available. In this report, using an in vivo living cell laser ablation technique, we show that Arabidopsis suspensor cells can develop into embryos after removing the embryo proper. The embryo proper plays a critical role in maintaining suspensor cell identity. However, this depends on the developmental stage; after the globular embryo stage, the suspensors no longer possess the potential to develop into embryos. We also reveal that hypophysis formation may be essential for embryo differentiation. Furthermore, we show that, after removing the embryo, auxin gradually accumulates in the top suspensor cell where cell division occurs to produce an embryo. Auxin redistribution likely reprograms the fate of the suspensor cell and triggers embryogenesis in suspensor cells. Thus, we provide direct evidence that the embryo suppresses the embryogenic potential of suspensor cells.

Genome-wide identification and characterization of cystatin family genes in rice (Oryza sativa L.)

11 Cystatin genes in rice were identified, and their expression patterns were comprehensively analyzed, which reveals multiple roles in both seed development and plant response to environmental variations. Cystatin is a group of small proteins and known to inhibit the activities of cysteine proteases in the papain C1A and legumain C13 peptidase families in plants. Cystatin family genes have only been well characterized recently in a few plant species such as Hordeum vulgare and Nicotiana tabacum, which show their critical roles in programmed cell death and responses to biotic stresses. Up to now, little is known about cystatin family genes and their roles in Oryza sativa, a model plant for cereal biology study. Here, we identified 11 cystatin genes in rice genome. Comprehensive expression profile analysis reveals that cystatin family genes in rice display diverse expression pattern. They are temporally regulated at different developmental stages during the process of seed production and germination. Our experiments also reveal that the majority of cystatin genes are responsive to plant hormones and different environmental cues including cold, drought and other abiotic stresses, while some others are very stable under different stresses, indicating their fundamental roles in normal plant development. In addition, their distribution in rice chromosomes and their evolutionary relation to the members of Cystatin family in A. thaliana and N. tabacum have also been analyzed. These works suggest multiple roles of cystatin family genes in both seed development and plant response to environmental variations.

The Maternal-to-Zygotic Transition in Higher Plants: Available Approaches, Critical Limitations, and Technical Requirements

Fertilization marks the turnover from the gametophyte to sporophyte generation in higher plants. After fertilization, sporophytic development undergoes genetic turnover from maternal to zygotic control: the maternal-to-zygotic transition (MZT). The MZT is thought to be critical for early embryogenesis; however, little is known about the time course or developmental impact of the MZT in higher plants. Here, we discuss what is known in the field and focus on techniques used in relevant studies and their limitations. Some significant questions and technical requirements for further investigations are also discussed.

Phytosulfokine peptide signaling controls pollen tube growth and funicular pollen tube guidance in Arabidopsis thaliana

Phytosulfokine (PSK) is a peptide growth factor that requires tyrosine sulfation carried out by tyrosylprotein sulfotransferase (TPST) for its activity. PSK is processed from precursor proteins encoded by five genes in Arabidopsis thaliana and perceived by receptor kinases encoded by two genes in Arabidopsis. pskr1-3 pskr2-1 and tpst-1 knockout mutants displayed reduced seed production, indicative of a requirement for PSK peptide signaling in sexual plant reproduction. Expression analysis revealed PSK precursor and PSK receptor gene activity in reproductive organs with strong expression of PSK2 in pollen. In support of a role for PSK signaling in pollen, in vitro pollen tube (PT) growth was enhanced by exogenously added PSK while PTs of pskr1-3 pskr2-1 and of tpst-1 were shorter. In planta, growth of wild-type pollen in pskr1-3 pskr2-1 and tpst-1 flowers appeared slower than growth in wild-type flowers. But PTs did eventually reach the base of the style, suggesting that PT elongation rate may not be responsible for the reduced fertility. Detailed analysis of anthers, style and ovules did not reveal obvious developmental defects. By contrast, a high percentage of unfertilized ovules in pskr1-3 pskr2-1 and in tpst-1 siliques displayed loss of funicular PT guidance, suggesting that PSK signaling is required to guide the PT from the transmitting tract to the embryo sac. Cross-pollination experiments with wild-type, pskr1-3 pskr2-1 and tpst-1 male and female parents revealed that both the PT and the female sporophytic tissue and/or female gametophyte contribute to successful PT guidance via PSK signaling and to fertilization success.

Characteristics and viral propagation properties of a new human diploid cell line, Walvax-2, and its suitability as a candidate cell substrate for vaccine production

Human diploid cell strains (HDCSs), possessing identical chromosome sets known to be free of all known adventitious agents, are of great use in developing human vaccines. However it is extremely difficult to obtain qualified HDCSs that can satisfy the requirements for the mass production of vaccines. We have developed a new HDCS, Walvax-2, which we derived from the lung tissue of a 3-month-old fetus. We established primary, master and working cell banks successfully from reconstituted frozen cells. Observations during the concurrent propagation of Walvax-2 and MRC-5 cells revealed differences in terms of growth rate, cell viability and viral sensitivities. Specifically, Walvax-2 cells replicated more rapidly than MRC-5 cells, with Walvax-2 cells attaining the same degree of confluence in 48 hours as was reached by MRC-5 cells in 72 hours. Moreover, Walvax-2 cells attained 58 passages of cell doublings whereas MRC-5 reached 48 passages during this period. We also assessed the susceptibility of these cells to rabies, hepatitis A, and Varicella viruses. Analysis of virus titers showed the Walvax-2 cells to be equal or superior to MRC-5 cells for cultivating these viruses. Furthermore, in order to characterize the Walvax-2 cell banks, a series of tests including cell identification, chromosomal characterization, tumorigenicity, as well as tests for the presence of microbial agents, exogenous viruses, and retroviruses, were conducted according to standard international protocols. In conclusion, results from this study show that Walvax-2 cell banks are a promising cell substrate and could potentially be used for the manufacturing of HDCVs.

Exogenous γ-aminobutyric acid (GABA) affects pollen tube growth via modulating putative Ca2+-permeable membrane channels and is coupled to negative regulation on glutamate decarboxylase

γ-Aminobutyric acid (GABA) is implicated in pollen tube growth, but the molecular and cellular mechanisms that it mediates are largely unknown. Here, it is shown that exogenous GABA modulates putative Ca(2+)-permeable channels on the plasma membranes of tobacco pollen grains and pollen tubes. Whole-cell voltage-clamp experiments and non-invasive micromeasurement technology (NMT) revealed that the influx of Ca(2+) increases in pollen tubes in response to exogenous GABA. It is also demonstrated that glutamate decarboxylase (GAD), the rate-limiting enzyme of GABA biosynthesis, is involved in feedback controls of Ca(2+)-permeable channels to fluctuate intracellular GABA levels and thus modulate pollen tube growth. The findings suggest that GAD activity linked with Ca(2+)-permeable channels relays an extracellular GABA signal and integrates multiple signal pathways to modulate tobacco pollen tube growth. Thus, the data explain how GABA mediates the communication between the style and the growing pollen tubes.

Inducible knock-down of GNOM during root formation reveals tissue-specific response to auxin transport and its modulation of local auxin biosynthesis

In plants, active transport of auxin plays an essential role in root development. Localization of the PIN1 auxin transporters to the basal membrane of cells directs auxin flow and depends on the trafficking mediator GNOM. GNOM-dependent auxin transport is vital for root development and thus offers a useful tool for the investigation of a possible tissue-specific response to dynamic auxin transport. To avoid pleiotropic effects, DEX-inducible expression of GNOM antisense RNA was used to disrupt GNOM expression transiently or persistently during embryonic root development. It was found that the elongation zone and the pericycle layer are the most sensitive to GNOM-dependent auxin transport variations, which is shown by the phenotypes in cell elongation and the initiation of lateral root primordia, respectively. This suggests that auxin dynamics is critical to cell differentiation and cell fate transition, but not to cell division. The results also reveal that GNOM-dependent auxin transport could affect local auxin biosynthesis. This suggests that local auxin biosynthesis may also contribute to the establishment of GNOM-dependent auxin gradients in specific tissues, and that auxin transport and local auxin biosynthesis may function together in the regulatory network for initiation and development of lateral root primordia. Thus, the data reveal a tissue-specific response to auxin transport and modulation of local auxin biosynthesis by auxin transport.