Analyses of the Molecular Mechanisms Associated with Silk Production in Silkworm by iTRAQ-Based Proteomics and RNA-Sequencing-Based Transcriptomics

The architecture of silk-secreting organs during the final larval stage of silkworms revealed by single-nucleus and spatial transcriptomics

Natural silks are renewable proteins with impressive mechanical properties and biocompatibility that are useful in various fields. However, the cellular and spatial organization of silk-secreting organs remains unclear. Here, we combined single-nucleus and spatially resolved transcriptomics to systematically map the cellular and spatial composition of the silk glands (SGs) of mulberry silkworms late in larval development. This approach allowed us to profile SG cell types and cell state dynamics and identify regulatory networks and cell-cell communication related to efficient silk protein synthesis; key markers were validated via transgenic approaches. Notably, we demonstrated the indispensable role of the ecdysone receptor (ultraspiracle) in regulating endoreplication in SG cells. Our atlas presents the results of spatiotemporal analysis of silk-secreting organ architecture late in larval development; this atlas provides a valuable reference for elucidating the mechanism of efficient silk protein synthesis and developing sustainable products made from natural silk.

Effect of acute exposure of Hg on physiological parameters and transcriptome expression in silkworms (Bombyx mori)

Mercury (Hg) contamination poses a global threat to the environment, given its elevated ecotoxicity. Herein, we employed the lepidopteran model insect, silkworm (Bombyx mori), to systematically investigate the toxic effects of Hg-stress across its growth and development, histomorphology, antioxidant enzyme activities, and transcriptome responses. High doses of Hg exposure induced evident poisoning symptoms, markedly impeding the growth of silkworm larvae and escalating mortality in a dose-dependent manner. Under Hg exposure, the histomorphology of both the midgut and fat body exhibited impairments. Carboxylesterase (CarE) activity was increased in both midgut and fat body tissues responding to Hg treatment. Conversely, glutathione S-transferase (GST) levels increased in the fat body but decreased in the midgut. The transcriptomic analysis revealed that the response induced by Hg stress involved multiple metabolism processes. Significantly differently expressed genes (DEGs) exhibited strong associations with oxidative phosphorylation, nutrient metabolisms, insect hormone biosynthesis, lysosome, ribosome biogenesis in eukaryotes, and ribosome pathways in the midgut or the fat body. The findings implied that exposure to Hg might induce the oxidative stress response, attempting to compensate for impaired metabolism. Concurrently, disruptions in nutrient metabolism and insect hormone activity might hinder growth and development, leading to immune dysfunction in silkworms. These insights significantly advance our theoretical understanding of the potential mechanisms underlying Hg toxicity in invertebrate organisms.

Identification of genes associated with the silk gland size using multi-omics in silkworm (Bombyx mori)

Silk gland size in silkworms (Bombyx mori) affects silk output. However, the molecular mechanisms by which genes regulate silk gland size remain unclear. In this study, silk glands from three pure silkworm strains (A798, A306 and XH) with different silk gland weight phenotypes were compared using transcriptomics and proteomics to identify differentially expressed genes (DEGs) and proteins (DEPs). When comparing A798 to A306 and A798 to XH, 830 and 469 DEGs were up-regulated, respectively. These genes were related to the gene ontology terms, metabolic process, transport activity and biosynthesis process. In addition, 372 and 302 up-regulated differentially expressed proteins were detected in A798 to A306 and A798 to XH, respectively, related to the gene ontology terms, ribosome and protein export, ribosome and polypeptide biosynthesis processes. Moreover, combined transcriptomics, proteomics and weighted correlation network analyses showed that five genes (BGIBMGA002524, BGIBMGA002629, BGIBMGA005659, BGIBMGA005711 and BGIBMGA010889) were significantly associated with the silk gland weight. Reverse Transcription-quantitative real-time Polymerase Chain Reaction (RT-qPCR) and Enzyme linked immunosorbent assay (ELISA) were used to verify the mRNA and protein expression of five genes in the silk glands and tissues of 18 silkworm strains. The results showed that four genes have higher expression levels in heavier silk glands. These genes are associated with glycogen metabolism, fatty acid synthesis and branched chain amino acid metabolism, thus potentially promoting growth and silk protein synthesis. These findings provide valuable insights into the molecular mechanisms underlying the relationship between silk gland weight and silk yield in silkworms.

The Study of Alanine Transaminase Activity in Tissues of Silkworm (Bombyx mori) via Direct Analysis in Real-Time (DART) Mass Spectrometry

Alanine transaminase (ALT) is an important amino acid-metabolizing enzyme in silkworm Bombyx mori L., and is mainly involved in transferring glutamate to alanine (serving as an essential precursor in silk protein synthesis) through transamination. Therefore, it is generally believed that silk protein synthesis in the silk gland and the cocoon quantity increase with the increase in ALT activity to a certain extent. Here, a novel analytical method was developed to determine the ALT activity in several key tissues of Bombyx mori L. including the posterior silk gland, midgut, fat body, middle silk gland, trachea and hemolymph, by combining the direct-analysis-in-real-time (DART) ion source with a triple-quadrupole mass spectrometer. In addition, a traditional ALT activity assay, the Reitman-Frankel method, was also used to measure ALT activity for comparison. The ALT activity results obtained via the DART-MS method are in good agreement with those obtained via the Reitman-Frankel method. However, the present DART-MS method provides a more convenient, rapid and environmentally friendly quantitative method for ALT measurement. Especially, this method can also monitor ALT activity in different tissues of Bombyx mori L. in real time.

Analysis of histomorphometric and proteome dynamics inside the silk gland lumen of Bombyx mori revealed the dynamic change of silk protein during the molt stage

Silkworms spin different silks at different growth stages for specific purposes. The silk spun before the end of each instar is stronger than that at the beginning of each instar and cocoon silk. However, the compositional changes in silk proteins during this process are unknown. Consequently, we performed histomorphological and proteomic analyses of the silk gland to characterize changes from the instar end to the next instar beginning. The silk glands were collected on day 3 of third- and fourth-instar larvae (III-3 and IV-3) and the beginning of fourth-instar larvae (IV-0). Proteomic analysis identified 2961 proteins from all silk glands. Silk proteins P25 and Ser5 were significantly more abundant in III-3 and IV-3 than in IV-0, and many cuticular proteins and protease inhibitors increased significantly in IV-0 compared with III-3 and IV-3. This shift may cause mechanical property differences between the instar end and beginning silk. Using section staining, qPCR, and western blotting, we found for the first time that silk proteins were degraded first and then resynthesized during the molting stage. Furthermore, we revealed that fibroinase mediated the changes of silk proteins during molting. Our results provide insights into the molecular mechanisms of silk proteins dynamic regulation during molting.

Comparative Silk Transcriptomics Illuminates Distinctive Impact of Artificial Selection in Silkworm Modern Breeding

Early domestication and the following improvement are two important processes in the cocoon silk evolution of silkworms. In contrast to early domestication, understanding of the improvement process is still fuzzy. By systematically comparing the larval silk gland transcriptomes of the wild, early domestic, and improved silkworms, we highlighted a novel landscape of transcriptome in the silk glands of improved ones. We first clarified that silk cocoon protein genes were up-regulated in modern breeding but not in early domestication. Furthermore, we found that differentially expressed genes (DEGs) between improved and early domestic silkworms (2711), as well as between improved and wild silkworms (2264), were obviously more than those between the early domestic and wild silkworms (158), with 1671 DEGs specific in the improved silkworm (IS-DEGs). Hierarchical clustering of all the DEGs consistently indicated that improved silkworms were significantly diverged from the early domestic and wild silkworms, suggesting that modern breeding might cause prompt and drastic dynamic changes of gene expression in the silk gland. We further paid attention to these 1671 IS-DEGs and were surprised to find that down-regulated genes were enriched in basic organonitrogen compound biosynthesis, RNA biosynthesis, and ribosome biogenesis processes, which are generally universally expressed, whereas those up-regulated genes were enriched in organonitrogen compound catabolic processes and functions involving in the dynamic regulation of protein post-translation of modification. We finally highlighted one candidate improvement gene among these up-regulated IS-DEGs, i.e., GDAP2, which may play roles in silk behavior and the overall robustness of the improved silkworm. The findings strongly suggest that modern breeding may facilitate effective control of the basic consumption of nitrogen and a stronger switch of nitrogen resources from other tissues to the silk glands, for an efficient supply for silk production, and implies the importance of brain behavior and robustness in silk yield improvement of modern breeding.

Comparative transcriptome and proteome reveal synergistic functions of differentially expressed genes and proteins implicated in an over-dominant silkworm heterosis of increased silk yield

We previously observed an over-dominant silkworm heterosis of increased yield in a cross of Bombyx mori nuclear polyhydrosis virus-resistant strain NB with a susceptible strain 306. In the present study, we found that heterosis also exists in crosses of NB with other susceptible strains, indicating it is a more general phenomenon. We performed comparative transcriptome and proteome and identified 1624 differentially expressed genes (DEGs) and 298 differentially expressed proteins (DEPs) in silk glands between parents and F1 hybrids, of which 24 DEGs/DEPs showed consistent expression at mRNA and protein levels revealed by Venn joint analysis. Their expressions are completely non-additive, mainly transgressive and under low-parent, suggesting recombination of parental genomes may be the major genetic mechanism for the heterosis. GO and KEGG analyses revealed that they may function in generally similar but distinctive aspects of metabolisms and processes with signal transduction and translation being most affected. Notably, they may not only up-regulate biosynthesis and transport of silk proteins but also down-regulate other unrelated processes, synergistically and globally remodelling the silk gland to increase yield and cause the heterosis. Our findings contribute insights into the understanding of silkworm heterosis and silk gland development and provide targets for transgenic manipulation to further increase the silk yield.

Revealing the difference of α-amylase and CYP6AE76 gene between polyphagous Conogethes punctiferalis and oligophagous C. pinicolalis by multiple-omics and molecular biological technique

Background

Conogethes pinicolalis has been thought as a Pinaceae-feeding variant of the yellow peach moth, Conogethes punctiferalis. The divergence of C. pinicolalis from the fruit-feeding moth C. punctiferalis has been reported in terms of morphology, ecology, and genetics, however there is a lack of detailed molecular data. Therefore, in this study, we investigated the divergence of C. pinicolalis from C. punctiferalis from the aspects of transcriptomics, proteomics, metabolomics and bioinformatics.

Results

The expression of 74,611 mRNA in transcriptome, 142 proteins in proteome and 218 metabolites in metabolome presented significantly differences between the two species, while the KEGG results showed the data were mainly closely related to metabolism and redox. Moreover, based on integrating system-omics data, we found that the α-amylase and CYP6AE76 genes were mutated between the two species. Mutations in the α-amylase and CYP6AE76 genes may influence the efficiency of enzyme preference for a certain substrate, resulting in differences in metabolic or detoxifying ability in both species. The qPCR and enzyme activity test also confirmed the relevant gene expression.

Conclusions

These findings of two related species and integrated networks provide beneficial information for further exploring the divergence in specific genes, metabolism, and redox mechanism. Most importantly, it will give novel insight on species adaptation to various diets, such as from monophagous to polyphagous.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08753-9.

Mechanism of the growth and development of the posterior silk gland and silk secretion revealed by mutation of the fibroin light chain in silkworm

Silkworm, as a model organism, has very high economic value due to its silk secretion ability. Although a large number of studies have attempted to elucidate the mechanism of silk secretion, it remains unclear. In this study, the fibroin light chain (Fib-L) gene of silkworm was subjected to CRISPR/Cas9 editing, which yielded premature termination of translation at 135 aa. Compared with those of the wild type, the posterior silk glands (PSGs) of the homozygous mutants on the third day of the fifth instar showed obvious premature degeneration. Comparative transcriptome and proteomic analyses of the PSGs of wild-type individuals, heterozygous mutants and homozygous mutants were performed on the fourth day of the fifth instar. A GO enrichment analysis showed that the differentially expressed genes (DEGs) between homozygous mutants and wild-type individuals were enriched in cytoskeleton-related terms, and a KEGG enrichment analysis showed that the upregulated DEGs between homozygous mutants and wild-type individuals were enriched in the phagosome and apoptosis pathways. These results indicated that apoptosis was activated prematurely in the PSGs of homozygous mutants. Furthermore, autophagy and heat shock response were activated in the PSGs of homozygous mutants, as demonstrated by an analysis of the DEGs related to autophagy and heat shock. A comparative proteomic analysis further confirmed that autophagy, apoptosis and the heat shock response were activated in the PSGs of homozygous mutants, which led to premature degradation of the PSGs. These results provide insights for obtaining a more in-depth understanding of the mechanism of silk secretion in silkworms.

Role of sericin 1 in the immune system of silkworms revealed by transcriptomic and proteomic analyses after gene knockout

The domestic silkworm is a type of lepidopteran insect that feeds on mulberry leaves and has high economic value because of its ability to spin cocoons. Sericin 1 is an important component of silkworm cocoons, accounting for approximately 25% of the material. In this study, CRISPR/Cas9‐mediated gene editing was successfully used to destroy the sericin 1 gene, and homozygous mutants were obtained after continuous screening. Homozygous mutation resulted in premature termination of the translation of sericin 1 protein at 323 amino acids. Comparative transcriptomic and proteomic analyses of middle silk gland cells from wild‐type individuals and mutants were performed on the fourth day of the fifth instar, and the results suggest that sericin 1 plays an important role in the cellular immune system. In addition, the results suggest that sericin 1 has a synergistic effect with some protease inhibitors and that the secretion of these proteins is strictly regulated. These results will provide new insights into the function and expression pattern of sericin 1 and the mechanism of silk secretion.

Comparative mRNA and LncRNA Analysis of the Molecular Mechanisms Associated With Low Silk Production in Bombyx mori

Naked pupa sericin and Naked pupa are two mutant strains of Bombyx mori with extremely low or no fibroin production compared to the Qiufeng and Baiyu strains, both of which exhibit very high silk fibroin production. However, the molecular mechanisms by which long non-coding RNAs regulate fibroin synthesis need further study. In this study, we performed high-throughput RNA-seq to investigate lncRNA and mRNA expression profiles in the posterior silk gland of Qiufeng, Baiyu, Nd-s^D, and Nd silkworms at the third day of the 5th instar. Our efforts yielded 26,767 novel lncRNAs and 6,009 novel mRNAs, the expression levels of silk protein genes and silk gland transcription factors were decreased in Qiufeng vs. Nd-s^D and Qiufeng vs. Nd, while those of many genes related to autophagy, apoptosis, RNA degradation, ubiquitin-mediated proteolysis and heat shock proteins were increased. Moreover, the expression of a large number of genes responsible for protein synthesis and secretion was significantly decreased in Nd. GO and KEGG analysis results showed that nucleotide excision repair, mRNA surveillance pathways, amino acid degradation, protein digestion and absorption, ER-associated degradation and proteasome pathways were significantly enriched for the Qiufeng vs. Nd-s^D and Qiufeng vs. Nd comparisons. In conclusion, our findings contribute to the lncRNA and mRNA database of Bombyx mori, and the identified differentially expressed mRNAs and lncRNAs help to reveal the molecular mechanisms of low silk production in Nd-s^D and Nd, providing new insights for improvement of silk yield and elucidation of silk mechanical properties.

Transcriptomics and proteomics-based analysis of heterosis on main economic traits of silkworm, Bombyx mori

The application of silkworm hybrids have promoted the innovation and development of agricultural technology, but the mechanism of heterosis in silkworm has not been explained clearly. In this study, the heterosis of silkworm in the aspects of body weight, silk gland and cocoon weight was investigated by means of silkworm hybridization and multi-omics approaches, including transcriptome and proteome. The results showed that heterosis of silkworm body weight, silk gland and cocoon weight was overdominant, but only part of genes and proteins were overdominant, and most of genes and proteins were non-additive. Combined analysis obtained six up-regulated genes and four down-regulated genes that were consistent both in transcriptome and proteome. Gene functional enrichment analysis indicated that most up-regulated genes and proteins were mostly related to metabolism, which led to accelerated metabolism and protein synthesis and contributing to improved heterosis. The up-regulation of 6-phosphate glucose dehydrogenase (G6PDH), phosphatidylethanolamine-binding protein (PEBP) and sHSP20.4, which are involved in metabolism, might be related to silk gland heterosis. SIGNIFICANCE: A combination of transcriptomic and proteomic analysis was used to understand the molecular mechanism of silkworm heterosis. We found that the phenotypic traits of silkworm are overdominant, while the analysis of transcriptome and proteome showed that only part of genes and proteins were overdominant, and most of genes and proteins were non-additive. Some of the genes had unique expression in F1, which was speculated that genes under heterozygous condition may result in rearrangement and cause metabolic changes in the hybrids. Those both up-regulated in transcriptomic and proteomic analysis were found to be involved in various metabolic processes, so as to accelerate metabolism and protein synthesis, thus exhibiting heterosis.

A transcriptome atlas of silkworm silk glands revealed by PacBio single-molecule long-read sequencing

The silk gland of the silkworm Bombyx mori is a specialized organ where silk proteins are efficiently synthesized under precise regulation that largely determines the properties of silk fibers. To understand the genes involved in the regulation of silk protein synthesis, considerable research has focused on the transcripts expressed in silk glands; however, the complete transcriptome profile of this organ has yet to be elucidated. Here, we report a full-length silk gland transcriptome obtained by PacBio single-molecule long-read sequencing technology. In total, 11,697 non-redundant transcripts were identified in mixed samples of silk glands dissected from larvae at five developmental stages. When compared with the published reference, the full-length transcripts optimized the structures of 3002 known genes, and a total of 9061 novel transcripts with an average length of 2171 bp were detected. Among these, 1403 (15.5%) novel transcripts were computationally revealed to be lncRNAs, 8135 (89.8%) novel transcripts were annotated to different protein and nucleotide databases, and 5655 (62.4%) novel transcripts were predicted to have complete ORFs. Furthermore, we found 1867 alternative splicing events, 2529 alternative polyadenylation events, 784 fusion events and 6596 SSRs. This study provides a comprehensive set of reference transcripts and greatly revises and expands the available silkworm transcript data. In addition, these data will be very useful for studying the regulatory mechanisms of silk protein synthesis.

Insights into the Synthesis, Secretion and Curing of Barnacle Cyprid Adhesive via Transcriptomic and Proteomic Analyses of the Cement Gland

Barnacles represent one of the model organisms used for antifouling research, however, knowledge regarding the molecular mechanisms underlying barnacle cyprid cementation is relatively scarce. Here, RNA-seq was used to obtain the transcriptomes of the cement glands where adhesive is generated and the remaining carcasses of Megabalanus volcano cyprids. Comparative transcriptomic analysis identified 9060 differentially expressed genes, with 4383 upregulated in the cement glands. Four cement proteins, named Mvcp113k, Mvcp130k, Mvcp52k and Mvlcp1-122k, were detected in the cement glands. The salivary secretion pathway was significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differentially expressed genes, implying that the secretion of cyprid adhesive might be analogous to that of saliva. Lysyl oxidase had a higher expression level in the cement glands and was speculated to function in the curing of cyprid adhesive. Furthermore, the KEGG enrichment analysis of the 352 proteins identified in the cement gland proteome partially confirmed the comparative transcriptomic results. These results present insights into the molecular mechanisms underlying the synthesis, secretion and curing of barnacle cyprid adhesive and provide potential molecular targets for the development of environmentally friendly antifouling compounds.

Synergism of open chromatin regions involved in regulating genes in Bombyx mori

The dynamic variability of transcription factors (TFs) and their binding sites makes it challenging to conduct genome-wide transcription regulation research. The silkworm Bombyx mori, which produces silk, is one of the most valuable model insects in the order Lepidoptera. The "opening" and "closing" of chromatin in different silk yield strains is associated with changes in silk production, making this insect a good model for studying the transcriptional regulation of genes. However, few studies have examined the open chromatin regions (OCRs) of silkworms, and studying OCR synergism and their function in silk production remains challenging. Here, we performed formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate OCRs from the silk glands of fifth-instar larvae of the DaZao and D872 strains. In total, 128,908 high confidence OCRs were identified and approximately 80% of OCRs were located in non-coding regions. OCRs upregulated adjacent genes and showed signal-dependent vulnerability to single-nucleotide polymorphisms. Mid- and low-signal OCRs were more likely to have single-nucleotide polymorphisms (SNP). Further, OCRs interacted with each other within a distance of 5 kb. We named the OCR interaction complex as the "cluster of related regions" (COREs). The functions of the CORE and its harbored OCRs showed some differences. Additionally, COREs enriched many silk protein synthesis-associated genes, some of which were upregulated. This study identified numerous high confidence regulation sites and synergistic regulatory modes of OCRs that affect adjacent genes. These results provide insight into silkworm transcriptional regulation and improve our understanding of cis-element cooperation.

New insight into the mechanism underlying the silk gland biological process by knocking out fibroin heavy chain in the silkworm

BACKGROUND

Exploring whether and how mutation of silk protein contributes to subsequent re-allocation of nitrogen, and impacts on the timing of silk gland degradation, is important to understand silk gland biology. Rapid development and wide application of genome editing approach in the silkworm provide us an opportunity to address these issues.

RESULTS

Using CRISPR/Cas9 system, we successfully performed genome editing of Bmfib-H. The loss-of-function mutations caused naked pupa and thin cocoon mutant phenotypes. Compared with the wild type, the posterior silk gland of mutant showed obviously degraded into fragments in advance of programmed cell death of silk gland cells. Comparative transcriptomic analyses of silk gland at the fourth day of the fifth instar larval stage(L5D4)identified 1456 differential expressed genes (DEGs) between posterior silk gland (PSG) and mid silk gland (MSG) and 1388 DEGs between the mutant and the wild type. Hierarchical clustering of all the DEGs indicated a remarkable down-regulated and an up-regulated gene clade in the mutant silk glands, respectively. Down-regulated genes were overrepresented in the pathways involved in cancer, DNA replication and cell proliferation. Intriguingly, up-regulated DEGs are significantly enriched in the proteasome. By further comparison on the transcriptome of MSG and PSG between the wild type and the mutant, we consistently observed that up-regulated DEGs in the mutant PSG were enriched in protein degrading activity and proteasome. Meantime, we observed a series of up-regulated genes involved in autophagy. Since these protein degradation processes would be normally occur after the spinning time, the results suggesting that these progresses were activated remarkably ahead of schedule in the mutant.

CONCLUSIONS

Accumulation of abnormal fib-H protein might arouse the activation of proteasomes as well as autophagy process, to promote the rapid degradation of such abnormal proteins and the silk gland cells. Our study therefore proposes a subsequent process of protein and partial cellular degradation caused by mutation of silk protein, which might be helpful for understanding its impact of the silk gland biological process, and further exploration the re-allocation of nitrogen in the silkworm.

QTL analysis of cocoon shell weight identifies BmRPL18 associated with silk protein synthesis in silkworm by pooling sequencing

Mechanisms that regulate silk protein synthesis provide the basis for silkworm variety breeding and silk gland bioreactor optimization. Here, using the pooling sequencing-based methodology, we deciphered the genetic basis for the varied silk production in different silkworm strains. We identified 8 SNPs, with 6 on chromosome 11 and 1 each on chromosomes 22 and 23, that were linked with silk production. After conducting an association analysis between gene expression pattern, silk gland development and cocoon shell weight (CSW), BMGN011620 was found to be regulating silk production. BMGN011620 encodes the 60S ribosomal protein, L18, which is an indispensable component of the 60S ribosomal subunit; therefore we named it BmRPL18. Moreover, the clustering of linked SNPs on chromosome 11 and the analysis of differentially expressed genes reported in previous Omics studies indicated that the genes regulating silk protein synthesis may exhibit a clustering distribution in the silkworm genome. These results collectively advance our understanding of the regulation of silk production, including the role of ribosomal proteins and the clustered distribution of genes involved in silk protein synthesis.

Data for transcriptomic and proteomic analyses of leaves from Clematis terniflora DC. under binary stress

High level of UV-B irradiation followed by dark treatment accumulates secondary metabolites in Clematis terniflora DC. To investigate the response mechanism under high level of UV-B irradiation followed by dark treatment, transcriptomic and proteomic analyses were performed in leaves of Clematis terniflora DC. The experimental design for the transcriptomic and proteomic analyses in leaves of C. terniflora under stresses was organized into a picture. For transcriptomics, mRNA-sequencing technology was used. Genes identified in leaves of C. terniflora at starting point, high level of UV-B irradiation, and high level of UV-B irradiation followed by dark treatment were listed; genes with different expression levels at starting point, high level of UV-B irradiation, and high level of UV-B irradiation followed by dark treatment were also presented in this DiB article. For proteomics, a gel-free/label-free proteomic technique was used. Proteins with different abundances in leaves at starting point, high level of UV-B irradiation, and high level of UV-B irradiation followed by dark treatment were presented in this DiB article. In order to monitor the expression levels of genes under the stress, quantitative reverse transcription polymerase chain reaction was performed. The primer sequences of genes selected for quantitative reverse transcription polymerase chain reaction was presented in this DiB article.

Complementary transcriptomic and proteomic analyses reveal regulatory mechanisms of milk protein production in dairy cows consuming different forages

Forage plays a critical role in the milk production of dairy cows; however, the mechanisms regulating bovine milk synthesis in dairy cows fed high forage rations with different basal forage types are not well-understood. In the study, rice straw (RS, low-quality) and alfalfa hay (AH, high-quality) diets were fed to lactating cows to explore how forage quality affected the molecular mechanisms regulating milk production using RNA-seq transcriptomic method with iTRAQ proteomic technique. A total of 554 transcripts (423 increased and 131 decreased) and 517 proteins (231 up-regulated and 286 down-regulated) were differentially expressed in the mammary glands of the two groups. The correlation analysis demonstrated seven proteins (six up-regulated and one down-regulated) had consistent mRNA expression. Functional analysis of the differentially expressed transcripts/proteins suggested that enhanced capacity for energy and fatty acid metabolism, increased protein degradation, reduced protein synthesis, decreased amino acid metabolism and depressed cell growth were related to RS consumption. The results indicated cows consuming RS diets may have had depressed milk protein synthesis because these animals had decreased capacity for protein synthesis, enhanced proteolysis, inefficient energy generation and reduced cell growth. Additional work evaluating RS- and AH-based rations may help better isolate molecular adaptations to low nutrient availability during lactation.