scholarly journals New insights into the proteins interacting with the promoters of silkworm fibroin genes

2021 ◽  
Author(s):  
Yan Ma ◽  
Qin Luo ◽  
Yao Ou ◽  
Yiyun Tang ◽  
Wenhui Zeng ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Silk Gland ◽  
Silk Protein ◽  
Human Society ◽  
Gene Promoters ◽  
Interacting Proteins ◽  
Fibroin Gene ◽  
Genes Encoding ◽  
Fibroin Light Chain ◽  
Synthesis Regulation

Abstract The silkworm, Bombyx mori, is a silk-producing insect that has contributed greatly to human society. The silk gland of B. mori is a specialized organ responsible for synthesizing silk fibroin and sericin proteins under control of numerous factors. However, which factors are involved in direct silk protein synthesis regulation remains largely unknown. We report the identification of promoter-interacting proteins (PIPs) necessary for the direct regulation of genes encoding fibroin proteins, including the fibroin heavy chain (fibH), fibroin light chain (fibL), and a 25-kD polypeptide protein (P25). In the fourth larval molting stage (M4) or day 5 fifth-instar larvae (L5D5), a total of 198, 292, and 247 or 330, 305, and 460 proteins binding to fibH, fibL and P25, respectively, were identified from the posterior silk gland by DNA pull-down combined with mass spectrometry. Many PIPs were particularly involved in ribosome-, metabolism- and disease-related pathways. Additionally, 135 and 212 proteins were identified as common PIPs of fibH, fibL and P25 in M4 and L5D5, respectively. Among all PIPs, we identified 31 potential transcription factors, such as Y-box and poly A-binding proteins, which play roles in nucleotide binding, ATP binding, or protein folding. This study provides the first in-depth profile of proteins interacting with fibroin gene promoters and contributes to a better understanding of silk protein synthesis regulation.

scholarly journals New insights into the proteins interacting with the promoters of silkworm fibroin genes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yan Ma ◽  
Qin Luo ◽  
Yao Ou ◽  
Yiyun Tang ◽  
Wenhui Zeng ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Silk Gland ◽  
Silk Protein ◽  
Human Society ◽  
Gene Promoters ◽  
Interacting Proteins ◽  
Fibroin Gene ◽  
Genes Encoding ◽  
Fibroin Light Chain ◽  
Synthesis Regulation

AbstractThe silkworm, Bombyx mori, is a silk-producing insect that has contributed greatly to human society. The silk gland of B. mori is a specialized organ responsible for synthesizing silk fibroin and sericin proteins under control of numerous factors. However, which factors are involved in direct silk protein synthesis regulation remains largely unknown. We report the identification of promoter-interacting proteins (PIPs) necessary for the regulation of genes encoding fibroin proteins, including the fibroin heavy chain (fibH), fibroin light chain (fibL), and a 25-kD polypeptide protein (P25). In the fourth larval molting stage (M4) or day 5 fifth-instar larvae (L5D5), a total of 198, 292, and 247 or 330, 305, and 460 proteins interacting with the promoter region of fibH, fibL and P25, respectively, were identified from the posterior silk gland by DNA pull-down combined with mass spectrometry. Many PIPs were particularly involved in ribosome- and metabolism-related pathways. Additionally, 135 and 212 proteins were identified as common PIPs of fibH, fibL and P25 in M4 and L5D5, respectively. Among all PIPs, we identified 31 potential transcription factors, such as Y-box and poly A-binding proteins, which play roles in nucleotide binding, ATP binding, or protein folding. This study provides the first in-depth profile of proteins interacting with fibroin gene promoters and contributes to a better understanding of silk protein synthesis regulation.

scholarly journals Deep Insight into the Transcriptome of the Single Silk Gland of Bombyx mori

2019 ◽  
Vol 20 (10) ◽  
pp. 2491 ◽  
Author(s):  
Run Shi ◽  
Sanyuan Ma ◽  
Ting He ◽  
Jian Peng ◽  
Tong Zhang ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Fatty Acid ◽  
Fatty Acid Biosynthesis ◽  
Silk Gland ◽  
Fiber Formation ◽  
Silk Fiber ◽  
Silk Protein ◽  
High Concentration ◽  
And Function ◽  
Source Use

The silk gland synthesizes and secretes a large amount of protein and stores liquid silk protein at an extremely high concentration. Interestingly, silk proteins and serine protease inhibitors are orderly arranged in the silk gland lumen and cocoon shells. Silk fiber formation and the spinning mechanism have not been fully elucidated. Therefore, we conducted a comparative transcriptome analysis of seven segments of the single silk gland to characterize internal changes in the silk gland during the 5th instar of mature larvae. In total, 3121 differentially expressed genes were identified in the seven segments. Genes highly expressed in the middle silk gland (MSG) were mainly involved in unsaturated fatty acid biosynthesis, fatty acid metabolism, apoptosis—fly, and lysosome pathways, whereas genes highly expressed in the posterior silk gland (PSG) were mainly involved in ribosome, proteasome, citrate cycle, and glycolysis/gluconeogenesis pathways. Thus, the MSG and PSG differ greatly in energy source use and function. Further, 773 gradually upregulated genes (from PSG to MSG) were involved in energy metabolism, silk protein synthesis, and secretion, suggesting that these genes play an important role in silk fiber formation. Our findings provide insights into the mechanism of silk protein synthesis and transport and silk fiber formation.

scholarly journals 40S ribosome profiling reveals distinct roles for Tma20/Tma22 (MCT-1/DENR) and Tma64 (eIF2D) in 40S subunit recycling

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
David J. Young ◽  
Sezen Meydan ◽  
Nicholas R. Guydosh
Keyword(s):  
Protein Synthesis ◽  
Neurological Disease ◽  
Ribosome Profiling ◽  
Minor Role ◽  
Stop Codons ◽  
Genes Encoding ◽  
Ribosome Footprinting ◽  
A Minor ◽  
And Control ◽  
In Cells

AbstractThe recycling of ribosomes at stop codons for use in further rounds of translation is critical for efficient protein synthesis. Removal of the 60S subunit is catalyzed by the ATPase Rli1 (ABCE1) while removal of the 40S is thought to require Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR). However, it remains unclear how these Tma proteins cause 40S removal and control reinitiation of downstream translation. Here we used a 40S ribosome footprinting strategy to directly observe intermediate steps of ribosome recycling in cells. Deletion of the genes encoding these Tma proteins resulted in broad accumulation of unrecycled 40S subunits at stop codons, directly establishing their role in 40S recycling. Furthermore, the Tma20/Tma22 heterodimer was responsible for a majority of 40S recycling events while Tma64 played a minor role. Introduction of an autism-associated mutation into TMA22 resulted in a loss of 40S recycling activity, linking ribosome recycling and neurological disease.

Participation of the upstream region of the fibroin gene in the formation of transcription complex in vitro

1986 ◽  
Vol 6 (11) ◽  
pp. 3928-3933
Author(s):  
M Tsuda ◽  
S Hirose ◽  
Y Suzuki
Keyword(s):  
Complex Formation ◽  
Specific Interaction ◽  
Inhibitory Effect ◽  
Silk Gland ◽  
Upstream Region ◽  
Fibroin Gene ◽  
Transcription Complexes ◽  
Posterior Silk Gland

The addition of exogenous histones has an inhibitory effect on fibroin gene transcription in posterior silk gland extracts. The histones probably disturb a process in complex formation, because when transcription complexes were constructed by preincubation of the templates with the extracts, the inhibitory effect of histones was greatly reduced. Transcription of a fibroin gene construct, pFb5' delta-238, having the upstream region beyond the TATA box was relatively less inhibited than that of pFb5' delta-44 lacking the upstream region. This tendency toward differential inhibition was observed in the silk gland extracts but not in a HeLa cell extract and persisted even after complex formation in the silk gland extracts, suggesting a specific interaction of the upstream region with some factors in the extracts. The complexes formed on pFb5' delta-44 are probably more susceptible to the inhibitory effect of histones. On the basis of these results we propose a participation of the upstream region of the fibroin gene in the formation of stable transcription complexes at the promoter through an interaction with specific factors in the silk gland. Since the transcription-enhancing effect via the upstream region is augmented at a high histone/DNA ratio, it may mimic the in vivo situation in which the fibroin gene can be transcribed in the posterior silk gland even in the presence of excess suppressive materials.

scholarly journals Elucidating the regulatory mechanism of Swi1 prion in global transcription and stress responses

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Zhiqiang Du ◽  
Jeniece Regan ◽  
Elizabeth Bartom ◽  
Wei-Sheng Wu ◽  
Li Zhang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Regulation Of Transcription ◽  
Interacting Proteins ◽  
Environmental Stress Response ◽  
Key Factors ◽  
Cellular Functions ◽  
Beneficial Effects ◽  
Genome Wide ◽  
Genes Encoding ◽  
A Subunit

AbstractTranscriptional regulators are prevalent among identified prions in Saccharomyces cerevisiae, however, it is unclear how prions affect genome-wide transcription. We show here that the prion ([SWI+]) and mutant (swi1∆) forms of Swi1, a subunit of the SWI/SNF chromatin-remodeling complex, confer dramatically distinct transcriptomic profiles. In [SWI+] cells, genes encoding for 34 transcription factors (TFs) and 24 Swi1-interacting proteins can undergo transcriptional modifications. Several TFs show enhanced aggregation in [SWI+] cells. Further analyses suggest that such alterations are key factors in specifying the transcriptomic signatures of [SWI+] cells. Interestingly, swi1∆ and [SWI+] impose distinct and oftentimes opposite effects on cellular functions. Translation-associated activities, in particular, are significantly reduced in swi1∆ cells. Although both swi1∆ and [SWI+] cells are similarly sensitive to thermal, osmotic and drought stresses, harmful, neutral or beneficial effects were observed for a panel of tested chemical stressors. Further analyses suggest that the environmental stress response (ESR) is mechanistically different between swi1∆ and [SWI+] cells—stress-inducible ESR (iESR) are repressed by [SWI+] but unchanged by swi1∆ while stress-repressible ESR (rESR) are induced by [SWI+] but repressed by swi1∆. Our work thus demonstrates primarily gain-of-function outcomes through transcriptomic modifications by [SWI+] and highlights a prion-mediated regulation of transcription and phenotypes in yeast.

scholarly journals Landscape Of HOXA Genes Methylation in Colorectal Cancer

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Muhiddin Ishak ◽  
Rashidah Baharudin ◽  
Loh Teng-Hern Tan ◽  
Learn-Han Lee ◽  
Nurul-Syakima Ab Mutalib
Keyword(s):  
Colorectal Cancer ◽  
Cancer Susceptibility ◽  
Cpg Islands ◽  
Methylation Pattern ◽  
Gene Promoters ◽  
Normal Tissues ◽  
Genes Encoding ◽  
Hoxa Genes ◽  
A Minor ◽  
Hoxa Gene

Colorectal cancer (CRC) is among the most common cancers worldwide and the second leading cause of cancer-related death in Malaysia. The HOXA gene cluster is a family of Homeobox A genes encoding transcriptional regulators that play vital roles in cancer susceptibility and progression. Dysregulated HOXA expression influences various aspects of carcinogenesis processes. Therefore, this study aims to elucidate the methylation landscape of HOXA genes in CRC. Twelve pairs of CRC — adjacent normal tissues were subjected to Infinium DNA MethyEPIC array. Differentially methylatedregions were identified using the ChAMP Bioconductor and methylation levels of HOXA genes were manually curated. We identified 100 significantly differentially methylated probes annotated to HOXA genes. HOXA3 has the highest number of differentially methylated probes (n=27), followed by HOXA2 (n=20) and HOXA4 (n=14). The majority (43%) of the probes were located at the transcription start site (TSS) 200, which is one of the gene promoters. In respect to CpG islands (CGI), the probes were equally located in the island and shore regions (47% each) while a minor percentage was in the shelf (6%). Our work gave a comprehensive assessment of the DNA methylation pattern of HOXA genes and provide the first evidence of HOXA2, HOXA3 and HOXA4 differential methylation in Malaysian CRC. The new knowledge from this study can be utilized to further increase our understanding of CRC methylomics, particularly on the homeobox A genes. The prognostic and diagnostic roles of the differentially methylated HOXA genes warrant future investigations.

Identification of an alpha-tubulin mutant of fission yeast from gamma-tubulin-interacting protein screening: genetic evidence for alpha-/gamma-tubulin interaction

2000 ◽  
Vol 113 (24) ◽  
pp. 4557-4562 ◽  
Author(s):  
A. Takeoka ◽  
M. Shimizu ◽  
T. Horio
Keyword(s):  
Fission Yeast ◽  
Central Element ◽  
Direct Interaction ◽  
Interacting Proteins ◽  
Microtubule Nucleation ◽  
Mutation Site ◽  
Interacting Protein ◽  
Alpha Tubulin ◽  
Genes Encoding ◽  
Gamma Tubulin

gamma-Tubulin has been determined to be a central element of microtubule nucleation and, thus, indispensable for cellular organization of the microtubule. Utilizing the fact that human gamma-tubulin can function in the fission yeast Schizosaccharomyces pombe, we have generated a unique mutant screening procedure which can specifically select mutants of genes encoding gamma-tubulin-interacting proteins. One of the isolated mutants, cs76, turned out to carry a mutation in the alpha 1-tubulin gene (nda2(+)). This result suggests a direct interaction between the alpha- and gamma-tubulins. We located the mutation site in the nda2 gene and characterized the mutant phenotype. Our results demonstrate the importance of the alpha-/gamma-tubulin interaction in microtubule nucleation and should complement previous knowledge.

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