Comprehensive transcriptome and proteome analyses reveal a novel sodium chloride responsive gene network in maize seed tissues during germination

Germination is a plant developmental process by which radicle of mature seeds start to penetrate surrounding barriers for seedling establishment and multiple environmental factors have been shown to affect it. Little is known how high salinity affects seed germination of C4 plant, Zea mays. Preliminary germination assay suggested that isolated embryo alone was able to germinate under 200 mM NaCl treatment, whereas the intact seeds were highly repressed. We hypothesized that maize endosperm may function in perception and transduction of salt signal to surrounding tissues such as embryo, showing a completely different response to that in Arabidopsis. Since salt response involves ABA, we analysed in vivo ABA distribution and quantity and the result demonstrated that ABA level in isolated embryo under NaCl treatment failed to increase in comparison with the water control, suggesting that the elevation of ABA level is an endosperm dependent process. Subsequently, by using advanced profiling techniques such as RNA sequencing and SWATH-MS-based quantitative proteomics, we found substantial differences in post-transcriptional and translational changes between salt-treated embryo and endosperm. In summary, our results indicate that these regulatory mechanisms, such as alternative splicing, are likely to mediate early responses to salt stress during maize seed germination.

[Effects of land use change on soil organic carbon and its components in karst rocky desertification of southwest China]

Soil organic carbon (SOC) is the dynamic medium of carbon transfer and the main pathway of carbon transfer in the karst ecosystem. SOC and its components are the important parts in soil carbon cycling of karst ecosystem. However, few studies have focused on SOC and its components in the karst ecosystem. We analyzed the effects of land use change on the SOC content, SOC reserve (SOCS), water-soluble organic carbon (WSOC), easily oxidizable organic carbon (EOC), particu-late organic carbon (POC), and light fraction organic carbon (LFOC), and heavy fraction organic carbon (HFOC) and their distribution ratio, with six different land-use patterns [Zanthoxylum bungeanum forest (HJ), Hylocereus undulates forest (HL), mixed forest of Z. bungeanum and H. undulates (HHL), Sabina chinensis forest (YB), mixed forest of S. chinensis and Ligustrum luci-dum (YBN), and slope cropland (PD)] in Huajiang Canyon of Guanling County, Guizhou Pro-vince. Results showed that SOC and SOCS in YB, YBN and HJ were significantly higher than those in HL, HHL and PD. In the 0-20 cm soil layer, the concentrations of SOCS followed the order of HJ＞YB＞YBN＞PD＞HHL＞HL. Contents of WSOC, EOC, POC, LFOC and HFOC in YB, YBN, and HJ were all higher than those in the other three patterns. Significant positive correlations existed between SOC and each of its components (WSOC, EOC, POC, LFOC and HFOC), also between any two of those components. Z. bungeanum could be used as a priority economic species for the ecological rehabilitation of karst rocky desertification and mountain agriculture development in Southwest China. WSOC, EOC, POC, LFOC and HFOC could be used as indicators of soil organic carbon pool.

Alternative splicing and translation play important roles in hypoxic germination in rice

Post-transcriptional mechanisms (PTMs), including alternative splicing (AS) and alternative translation initiation (ATI), may explain the diversity of proteins involved in plant development and stress responses. Transcriptional regulation is important during the hypoxic germination of rice seeds, but the potential roles of PTMs in this process have not been characterized. We used a combination of proteomics and RNA sequencing to discover how AS and ATI contribute to plant responses to hypoxia. In total, 10 253 intron-containing genes were identified. Of these, ~1741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds compared with controls. Over 95% of these were not present in the list of differentially expressed genes. In particular, regulatory pathways such as the spliceosome, ribosome, endoplasmic reticulum protein processing and export, proteasome, phagosome, oxidative phosphorylation, and mRNA surveillance showed substantial AS changes under hypoxia, suggesting that AS responses are largely independent of transcriptional regulation. Considerable AS changes were identified, including the preferential usage of some non-conventional splice sites and enrichment of splicing factors in the DAS data sets. Taken together, these results not only demonstrate that AS and ATI function during hypoxic germination but they have also allowed the identification of numerous novel proteins/peptides produced via ATI.

Genome-wide identification and functional analysis of the splicing component SYF2/NTC31/p29 across different plant species

This study systematically identifies plant SYF2/NTC31/p29 genes from 62 plant species by a combinatory bioinformatics approach, revealing the importance of this gene family in phylogenetics, duplication, transcriptional, and post-transcriptional regulation. Alternative splicing is a post-transcriptional regulatory mechanism, which is critical for plant development and stress responses. The entire process is strictly attenuated by a complex of splicing-related proteins, designated splicing factors. Human p29, also referred to as synthetic lethal with cdc forty 2 (SYF2) or the NineTeen complex 31 (NTC31), is a core protein found in the NTC complex of humans and yeast. This splicing factor participates in a variety of biological processes, including DNA damage repair, control of the cell cycle, splicing, and tumorigenesis. However, its function in plants has been seldom reported. Thus, we have systematically identified 89 putative plant SYF2s from 62 plant species among the deposited entries in the Phytozome database. The phylogenetic relationships and evolutionary history among these plant SYF2s were carefully examined. The results revealed that plant SYF2s exhibited distinct patterns regarding their gene structure, promoter sequences, and expression levels, suggesting their functional diversity in response to developmental cues or stress treatments. Although local duplication events, such as tandem duplication and retrotransposition, were found among several plant species, most of the plant species contained only one copy of SYF2, suggesting the existence of additional mechanisms to confer duplication resistance. Further investigation using the model dicot and monocot representatives Arabidopsis and rice SYF2s indicated that the splicing pattern and resulting protein isoforms might play an alternative role in the functional diversity.

Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants

BACKGROUND

The next-generation sequencing (NGS) technology has greatly facilitated genomic and transcriptomic studies, contributing significantly in expanding the current knowledge on genome and transcriptome. However, the continually evolving variety of sequencing platforms, protocols and analytical pipelines has led the research community to focus on cross-platform evaluation and standardization. As a NGS pioneer in China, the Beijing Genomics Institute (BGI) has announced its own NGS platform designated as BGISEQ-500, since 2016. The capability of this platform in large-scale DNA sequencing and small RNA analysis has been already evaluated. However, the comparative performance of BGISEQ-500 platform in transcriptome analysis remains yet to be elucidated. The Illumina series, a leading sequencing platform in China's sequencing market, would be a preferable reference to evaluate new platforms.

METHODS

To this end, we describe a cross-platform comparative study between BGISEQ-500 and Illumina HiSeq4000 for analysis of Arabidopsis thaliana WT (Col 0) transcriptome. The key parameters in RNA sequencing and transcriptomic data processing were assessed in biological replicate experiments, using aforesaid platforms.

RESULTS

The results from the two platforms BGISEQ-500 and Illumina HiSeq4000 shared high concordance in both inter- (correlation, 0.88-0.93) and intra-platform (correlation, 0.95-0.98) comparison for gene quantification, identification of differentially expressed genes and alternative splicing events. However, the two platforms yielded highly variable interpretation results for single nucleotide polymorphism and insertion-deletion analysis.

CONCLUSION

The present case study provides a comprehensive reference dataset to validate the capability of BGISEQ-500 enabling it to be established as a competitive and reliable platform in plant transcriptome analysis.

Natural variation in the promoter of rice calcineurin B-like protein10 (OsCBL10) affects flooding tolerance during seed germination among rice subspecies

Rice (Oryza sativa L.) has two ecotypes, upland and lowland rice, that have been observed to show different tolerance levels under flooding stress. In this study, two rice cultivars, upland (Up221, flooding-intolerant) and lowland (Low88, flooding-tolerant), were initially used to study their molecular mechanisms in response to flooding germination. We observed that variations in the OsCBL10 promoter sequences in these two cultivars might contribute to this divergence in flooding tolerance. Further analysis using another eight rice cultivars revealed that the OsCBL10 promoter could be classified as either a flooding-tolerant type (T-type) or a flooding-intolerant type (I-type). The OsCBL10 T-type promoter only existed in japonica lowland cultivars, whereas the OsCBL10 I-type promoter existed in japonica upland, indica upland and indica lowland cultivars. Flooding-tolerant rice cultivars containing the OsCBL10 T-type promoter have shown lower Ca²⁺ flow and higher α-amylase activities in comparison to those in flooding-intolerant cultivars. Furthermore, the OsCBL10 overexpression lines were sensitive to both flooding and hypoxic treatments during rice germination with enhanced Ca²⁺ flow in comparison to wild-type. Subsequent findings also indicate that OsCBL10 may affect OsCIPK15 protein abundance and its downstream pathways. In summary, our results suggest that the adaptation to flooding stress during rice germination is associated with two different OsCBL10 promoters, which in turn affect OsCBL10 expression in different cultivars and negatively affect OsCIPK15 protein accumulation and its downstream cascade.

Physiological changes and sHSPs genes relative transcription in relation to the acquisition of seed germination during maturation of hybrid rice seed

BACKGROUND

During the production of early hybrid rice seed, the seeds dehydrated slowly and retained high moisture levels when rainy weather lasted for a couple of days, and the rice seeds easily occurred pre-harvest sprouting (PHS) along with high temperature. Therefore it is necessary to harvest the seeds before the PHS occurred.

RESULTS

The seeds of hybrid rice (Oryza sativa L. subsp. indica) cv. Qianyou No1 that harvests from 19 to 28 days after pollination (DAP) all had high seed vigour. The seed moisture content at 10 DAP was 36.1%, and declined to 28.6% at 19 DAP; the contents of soluble sugar and total starch increased significantly with the development of seeds. The soluble protein content, the level of abscisic acid (ABA) and gibberellin (GA3 ), and ascorbate peroxidase (APX) activity continued to decrease from 10 DAP to 19 DAP. The seeds at 19 DAP had the highest peroxidase (POD) activity and lowest catalase (CAT) activity while the superoxide dismutase (SOD) activity had no significant difference among the different developing periods. The relative expressions of genes 64S Hsp18.0 and Os03g0267200 transcripts increased significantly from 10 to 19 DAP, and then decreased. However, no significant change was recorded in soluble protein, sugar and GA3 after 16 DAP, and they all significantly correlated with seed viability and vigour during the process of seed maturity.

CONCLUSION

The seeds of hybrid rice Qianyou No1 had a higher viability and vigour when harvested from 19 DAP to 28 DAP, the transcription levels of 64S Hsp18.0 and Os03g0267200 increased significantly from 10 DAP to 19 DAP and the highest value was recorded at 19 DAP. The seeds could be harvested as early as 19 DAP without negative influence on seed vigour and viability.

Energetics and dynamics of threshold photoion-pair formation in HF∕DF

Threshold ion-pair production spectroscopy (TIPPS) has been applied to two isotopomers, HF and DF. From the high resolution (approximately 0.3 cm(-1)) TIPP spectra, the ion-pair thresholds of HFDF have been precisely measured. Combined with the ionization energy of H(D), the electron affinity of F, and the zero point energies of HFDF, the difference between their classical bond dissociation energies was obtained as D(e)(H-F)-D(e)(D-F) = 12.4 +/- 0.5 cm(-1). Our result provides an experimental estimate of the Born-Oppenheimer breakdown in the ground electronic state. The present work also measured the total ion-pair yield spectra of HF and DF in the threshold region, and the ion-pair formation mechanisms of these two molecules were discussed in light of the high resolution results.

Threshold ion-pair production spectroscopy of HCN

The spectroscopic technique of threshold ion-pair production spectroscopy (TIPPS) has been applied to the triatomic molecule HCN. We have recorded the total ion-pair yield and TIPP spectra for the HCN-->H(+) + CN(-) process using coherent vacuum ultraviolet excitation. From the simulation of our high-resolution TIPP spectrum we have precisely measured the HCN ion-pair threshold E(IP) (0) to be 122 244 +/- 4 cm(-1). This value could be used to determine the bond dissociation energy D(0)(H-CN) to unprecedented accuracy. Our fitting result also showed that rotationally excited instead of cold CN(-) fragment is favored as the ion-pair dissociation product in the threshold region.

Threshold ion-pair production spectroscopy (TIPPS) of H2 and D2

The threshold ion-pair production spectra at the J" = 0 and J" = 1 thresholds of H2 and J" = 0, 1 and 2 thresholds of D2 obtained with single photon excitation are presented. The ion-pair yield spectra of H2 and D2 over these energy ranges demonstrate strong resonant enhancement, parts of which dominate the TIPPS signals, permitting the assignment of the lower states of these resonances. From those thresholds with weak resonant enhancement (the J" = 0 threshold of H2 and the J" = 1 threshold of D2) a very small direct contribution to ion-pair production can be observed. The behaviour of the TIPPS spectra taken with different applied discrimination fields is understood by modeling the field ionization behaviour of a MATI spectrum of H2, containing both the similarly resonantly enhanced v+ = 8 S(0) ionization threshold and the non-resonantly enhanced S(1) ionization threshold. From the H2 J" = 1 and D2 J" = 0 TIPPS spectra the energetic field-free thresholds of the H2 and D2 ion-pair limits were determined to be 139,714.8 +/- 1.0 cm-1 and 140,370.2 cm-1 +/- 1.0 cm-1, respectively.

The adjacent pixel nonlinearity: problems and solutions

The adjacent pixel nonlinearity refers to the dependence of the luminance of a given pixel on the preceding pixel or pixels. We measured this nonlinearity for two CRT displays by measuring the average luminances of a variety of test patterns with different luminance jumps. A two-stage model proposed by Mulligan and Stone was used to fit the data [Mulligan, J.B. & Stone, L. S., (1989). Journal of the Optical Society of America A, 6, 1217-1227 (1989)]. The results show that the model predicts our data well. Based on our measurements and the modeling results, a double-entry look-up table was created to compensate for this nonlinearity. This compensation method works even if the current pixel depends on more than one preceding pixel. Observers commented that at small pixel sizes the compensation results in a sharp, accurate image. Advantages and problems of this compensation will be discussed.

The retinoblastoma protein physically associates with the human cdc2 kinase

The protein product (pRB) of the retinoblastoma susceptibility gene functions as a negative regulator of cell proliferation, and its activity appears to be modulated by phosphorylation. Using a new panel of anti-human pRB monoclonal antibodies, we have investigated the biochemical properties of this protein. These antibodies have allowed us to detect a pRB-associated kinase that has been identified as the cell cycle-regulating kinase p34cdc2 or a closely related enzyme. Since this associated kinase phosphorylates pRB at most of the sites used in vivo, these results suggest that this kinase is one of the major regulators of pRB. The associated kinase activity follows the pattern of phosphorylation seen for pRB in vivo. The associated kinase activity is not seen in the G1 phase but appears in the S phase, and the levels continue to increase throughout the remainder of the cell cycle.

Antibodies specific for the human retinoblastoma protein identify a family of related polypeptides

Even though the retinoblastoma gene is one of the best-studied tumor suppressor genes, little is known about its functional role. Like all tumor suppressor gene products, the retinoblastoma protein (pRB) is thought to inhibit some aspect of cell proliferation. It also appears to be a cellular target of several DNA tumor virus-transforming proteins, such as adenovirus E1A, human papillomavirus E7, or simian virus 40 large T antigen. To help in the analysis of pRB, we have prepared a new set of anti-human pRB monoclonal antibodies. In addition to being useful reagents for the study of human pRB, these antibodies display several unexpected properties. They can be used to distinguish different subsets of the pRBs on the basis of their phosphorylation states. Some are able to recognize pRB homologs in other species, including mice, chickens, and members of the genus Xenopus. In addition, some of these antibodies can bind directly to other cellular proteins that, like pRB, were originally identified through their association with adenovirus E1A. These immunologically cross-reactive proteins include the p107 and p300 proteins, and their recognition by antibodies raised against pRB suggests that several members of the E1A-targeted cellular proteins form a structurally and functionally related family.

The regions of the retinoblastoma protein needed for binding to adenovirus E1A or SV40 large T antigen are common sites for mutations

The protein product of the retinoblastoma (RB) gene is thought to function in a pathway that restricts cell proliferation. Recently, transforming proteins from three different classes of DNA tumor viruses have been shown to form complexes with the RB protein. Genetic studies suggest that these interactions with the RB protein are important steps in transformation by these viruses. In order to understand better the function of the RB-viral oncoprotein complexes, we have mapped the regions of the RB protein that are necessary for these associations. Two non-contiguous regions of RB were found to be essential for complex formation with adenovirus E1A or SV40 large T antigen. These two regions are found between amino acids 393 and 572 and 646 and 772. Interestingly, these binding sites on RB overlap with the positions of naturally occurring, inactivating mutations of the RB gene. These results strongly suggest that these viral oncoproteins are targeting a protein domain that is an important site in the normal function of the RB protein.