Cheng Song

West Anhui University

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Muhammad Aamir Manzoor

Shanghai Jiao Tong University

Bangxing Han

West Anhui University

Yingyu Zhang

First Affiliated Hospital of Henan University of Science and Technology

Cunwu Chen

Anhui University of Traditional Chinese Medicine

Haoyu Pan

West Anhui University

Peipei Wei

Changzhi University

Irfan Ali Sabir

Ministry of Agriculture and Rural Affairs

Yongping Cai

Anhui Agricultural University

Bangxing Han

Anhui University of Traditional Chinese Medicine

Jun Dai

Zunyi Medical University

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West Anhui University

Anhui University of Traditional Chinese Medicine

Anhui Agricultural University

Novartis (United States)

Chinese Academy of Sciences

Novartis (Switzerland)

Ministry of Agriculture and Rural Affairs

Chinese Academy of Medical Sciences & Peking Union Medical College

Novartis Institutes for BioMedical Research

Chinese Academy of Agricultural Sciences

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Genome-wide identification and expression analysis of TIFY genes under MeJA, cold and PEG-induced drought stress treatment in Dendrobium huoshanense

Physiology and Molecular Biology of Plants (2024)

Guohui Li Muhammad Aamir Manzoor Rui Chen Yingyu Zhang Cheng Song

plant evolution

Methyl jasmonate

Segmental duplication

Functional divergence

Concerted evolution

Negative selection

10.1007/s12298-024-01442-9

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Citations (4)

Sequence Analysis of WRKY Transcription Factor Family in Dendrobium officinale

bioRxiv (Cold Spring Harbor Laboratory) (2022)

Haoyu Pan Yeyuan Feng Liangwen Wei Xinxin Sun Shili Tao

Abstract WRKY transcription factors are a key class of plant regulators that regulate Dendrobium growth, development, and stress tolerance. In this work, 74 Dendrobium WRKY genes were found in the Dendrobium whole genome file using tbtools software, hmmer3.0 software, pfam website, mega6.0 software, genedoc software, meme online analysis website, and other tools, and tbtools software was utilized after amino acid alignment. A phylogenetic tree of the Dendrobium and Arabidopsis WRKY transcription factors’ sequence alignment was built, as well as the chromosomal location, gene structure analysis, conserved domain analysis, and cis-acting element analysis of the Dendrobium WRKY gene. The phylogenetic tree comparison analysis revealed that Dendrobium WRKY transcription factors were classified into three groups: I, II, and III, with Group II subdivided into five subgroups: II-a, II-b, II-c, II-d, and II-e. According to amino acid alignment research, the Dendrobium WRKY transcription factor contains a highly conserved WRKYGQK sequence. According to gene chromosomal mapping, the Dendrobium WRKY gene was found to be irregularly distributed across many chromosomes of Dendrobium officinale. Introns vary greatly in terms of quantity and starting place. According to conserved domain analysis, the Dendrobium WRKY gene comprised diverse patterns in number and species, but all had the conserved domain WRKYGQK, and there were certain distinguishing motifs amongst subfamilies. Elements with a cis-action It was found that the Dendrobium WRKY gene has a lot of cis-acting elements, like light response, low temperature stress response, drought response, hormone response, growth differentiation responses.

WRKY protein domain

Dendrobium

10.1101/2022.04.10.487774

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Underlying mechanism of Dendrobium huoshanense resistance to lead stress using the quantitative proteomics method

BMC Plant Biology (2024)

Cheng Song Juncheng Dai Yanshuang Ren Muhammad Aamir Manzoor Yingyu Zhang

Lead affects photosynthesis and growth and has serious toxic effects on plants. Here, the differential expressed proteins (DEPs) in D. huoshanense were investigated under different applications of lead acetate solutions. Using label-free quantitative proteomics methods, more than 12,000 peptides and 2,449 proteins were identified. GO and KEGG functional annotations show that these differential proteins mainly participate in carbohydrate metabolism, energy metabolism, amino acid metabolism, translation, protein folding, sorting, and degradation, as well as oxidation and reduction processes. A total of 636 DEPs were identified, and lead could induce the expression of most proteins. KEGG enrichment analysis suggested that proteins involved in processes such as homologous recombination, vitamin B6 metabolism, flavonoid biosynthesis, cellular component organisation or biogenesis, and biological regulation were significantly enriched. Nearly 40 proteins are involved in DNA replication and repair, RNA synthesis, transport, and splicing. The effect of lead stress on D. huoshanense may be achieved through photosynthesis, oxidative phosphorylation, and the production of excess antioxidant substances. The expression of 9 photosynthesis-related proteins and 12 oxidative phosphorylation-related proteins was up-regulated after lead stress. Furthermore, a total of 3 SOD, 12 POD, 3 CAT, and 7 ascorbate-related metabolic enzymes were identified. Under lead stress, almost all key enzymes involved in the synthesis of antioxidant substances are up-regulated, which may facilitate the scavenging of oxygen-free radical scavenging. The expression levels of some key enzymes involved in sugar and glycoside synthesis, the phenylpropanoid synthesis pathway, and the terpene synthesis pathway also increased. More than 30 proteins involved in heavy metal transport were also identified. Expression profiling revealed a significant rise in the expression of the ABC-type multidrug resistance transporter, copper chaperone, and P-type ATPase with exposure to lead stress. Our findings lay the basis for research on the response and resistance of D. huoshanense to heavy metal stress.

Phenylpropanoid

KEGG

Metabolic pathway

Proteome

10.1186/s12870-024-05476-9

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Mitochondrial outer and inner membrane fusion requires a modified carrier protein

The Journal of Cell Biology (2009)

Suzanne Hoppins Jennifer S. Horner Cheng Song J. Michael McCaffery Jodi Nunnari

In yeast, three proteins are essential for mitochondrial fusion. Fzo1 and Mgm1 are conserved guanosine triphosphatases that reside in the outer and inner membranes, respectively. At each membrane, these conserved proteins are required for the distinct steps of membrane tethering and lipid mixing. The third essential component is Ugo1, an outer membrane protein in the mitochondrial transport protein family. We show that Ugo1 is a modified member of this family, containing three transmembrane domains and existing as a dimer, a structure that is critical for the fusion function of Ugo1. Our functional analysis of Ugo1 indicates that it is required distinctly for both outer and inner membrane fusion after membrane tethering, indicating that it operates at the lipid-mixing step of fusion. This role is distinct from the fusion dynamin-related proteins and thus demonstrates that at each membrane, a single fusion protein is not sufficient to drive the lipid-mixing step, but instead, this step requires a more complex assembly of proteins.

Mitochondrial carrier

Peripheral membrane protein

Inner membrane

10.1083/jcb.200809099

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Citations (85)

Plant AT-rich protein and zinc-binding protein (PLATZ) family in Dendrobium huoshanense: identification, evolution and expression analysis

BMC Plant Biology (2024)

Fangli Gu Yanshuang Ren Muhammad Aamir Manzoor Tingting Wang Renshu Huang

PLATZ (plant A/T-rich protein and zinc-binding protein) transcription factors are essential for plant growth, development, and responses to abiotic stress. The regulatory role of PLATZ genes in the environmental adaptation of D. huoshanense is inadequately comprehended. The genome-wide identification of D. huoshanense elucidates the functions and regulatory processes of the gene family. Our investigation encompassed the examination of PLATZ gene structures and chromosome distribution, the construction of the phylogenetic tree with its relatives, and the analysis of the cis-acting elements and expression profiles potentially implicated in growth and stress responses. Eleven DhPLATZs were classified into three clades (I, II, and III) according to their evolutionary homology. The distribution of these genes over six chromosomes indicated that both whole genome duplication (WGD) and segmental duplication events have contributed to the expansion of this gene family. The Ka/Ks analysis revealed a pattern of purifying selection after duplication occurrences, suggesting little alterations in functional divergence. The collinearity and microsynteny results revealed that the three DhPLATZ genes shared the same conserved domains as the paralogs from D. huoshanense and D. chrysotoxum. Expression profiling and quantitative analysis demonstrated that DhPLATZ genes had unique expression patterns in response to phytohormones and cold stress. Subcellular localization indicated that three DhPLATZ genes were expressed in the nucleus, suggesting their role as transcription factors. These findings enhance our understanding of PLATZ genes' involvement in D. huoshanense species and underscore their significance as important areas for further research.

Functional divergence

Segmental duplication

Homology

10.1186/s12870-024-06009-0

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Genome-scale identification, expression and evolution analysis of B-box members in Dendrobium huoshanense

Heliyon (2024)

Hui Deng Yingyu Zhang Muhammad Aamir Manzoor Irfan Ali Sabir Bangxing Han

B-box (BBX) proteins have been recognized as vital determinants in plant development, morphogenesis, and adaptive responses to a myriad of environmental stresses. These zinc-finger proteins play a pivotal role in various biological processes. Their influence spans photomorphogenesis, the regulation of flowering, and imparting resilience to a wide array of challenges, encompassing both biotic and abiotic factors. Chromosome localization, gene structure and conserved motifs, phylogenetic analysis, collinearity analysis, expression profiling, fluorescence quantitative analysis, and tobacco transient transformation methods were used for functional localization and expression pattern analysis of the DhBBX gene. A total of 23 DhBBX members were identified from Dendrobium huoshanense. Subsequent phylogenetic evaluations effectively segregated these genes into five discrete evolutionary subsets. The predictions of subcellular localizations revealed that all these proteins were localized in the nucleus. The genetic composition and patterns showed that the majority of these genes consisted of several exons, with a few variations that could be attributed to transposon insertion. A comprehensive analysis using qRT-PCR was conducted to unravel the expression patterns of these genes in D. huoshanense, with a specific concentration on their responses to various hormone treatments and cold stress. Subcellular localization reveals that DhBBX21 and DhBBX9 are located in the nucleus. Our results provide a deep comprehension of the complex regulatory mechanisms of BBXs in response to various environmental and hormonal stimuli. These discoveries encourage further detailed and focused investigations into the operational dynamics of the BBX gene family in a wider range of plant species.

10.1016/j.heliyon.2024.e32773

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Citations (1)

Basic components detection of Dendrobium plants v1

Cheng Song

Dendrobium

10.17504/protocols.io.h4gb8tw

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Citations (0)

Genomic data from Chinese cabbage (Brassica rapa)

X. Wang Han Wang J. Wang Rujian Sun J. Y. Wu

Brassica rapa

Source

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Data notes on the proteomics of Dendrobium huoshanense under pb treatment

BMC Genomic Data (2024)

Jun Dai Yingyu Zhang Yunpeng Zhang Yan Wang Xiaoyuan Ding

Abstract Objectives Pb stress has a negative impact on plant growth by interfering with photosynthesis and releasing reactive oxygen species, causing major risks such as heavy metal ion accumulation in the soil matrix. A proteomics experiment was conducted to determine whether protein levels of Dendrobium huoshanense changed in response to Pb stress seven to fifteen days after being sprayed with a 200 mg/L Pb (NO 3 ) 2 solution. The proteomic data we gathered provides a model for investigations into the mechanisms underlying Dendrobium plant resistance to heavy metal stress. Data description A label-free quantitative proteomics approach was employed to examine the variations in protein expression levels of D. huoshanense at different times of Pb(NO 3 ) 2 treatment. We submitted the raw data obtained from these proteomics sequencing experiments to the ProteomeXchange database with the accession number PXD047050. 63,194 mass spectra in total were compared after being imported into the Proteome Discoverer software for database search. A total of 12,402 spectral peptides were identified with a confidence level exceeding 99%, which resulted in the identification of 2,449 significantly differential proteins. These proteins can be utilized for screening, functional annotation, and enrichment analysis of differentially expressed proteins before and after heavy metal treatment experiments.

Proteome

10.1186/s12863-024-01205-1

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A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data

Genome Biology and Evolution (2020)

Bangxing Han Jing Yi Jun Dai Tao Zheng Fangli Gu

Abstract Dendrobium huoshanense is used to treat various diseases in traditional Chinese medicine. Recent studies have identified active components. However, the lack of genomic data limits research on the biosynthesis and application of these therapeutic ingredients. To address this issue, we generated the first chromosome-level genome assembly and annotation of D. huoshanense. We integrated PacBio sequencing data, Illumina paired-end sequencing data, and Hi-C sequencing data to assemble a 1.285 Gb genome, with contig and scaffold N50 lengths of 598 kb and 71.79 Mb, respectively. We annotated 21,070 protein-coding genes and 0.96 Gb transposable elements, constituting 74.92% of the whole assembly. In addition, we identified 252 genes responsible for polysaccharide biosynthesis by Kyoto Encyclopedia of Genes and Genomes functional annotation. Our data provide a basis for further functional studies, particularly those focused on genes related to glycan biosynthesis and metabolism, and have implications for both conservation and medicine.

Sequence assembly

Gene Annotation

KEGG

10.1093/gbe/evaa215

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Citations (37)