Review
Plant Sciences
Juriaan Rienstra, Jorge Hernandez-Garcia, Dolf Weijers
Summary: Most plant growth and development processes are regulated by auxin, with the nuclear auxin pathway (NAP) being the most well-studied mechanism. In this pathway, Auxin Response Factors (ARFs) determine which genes become auxin regulated by binding to specific DNA sequences. Recent studies have revealed the DNA binding specificities of different ARFs and the minimal functional system of the NAP system. This review provides an overview of key aspects of ARF DNA binding and highlights the importance of studying minimal NAP systems and algal ARFs, as well as using cutting-edge techniques and structural biology to further understand ARF function.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Wenjun Sun, Min Yao, Zhen Wang, Ying Chen, Junyi Zhan, Jun Yan, Shuangqing Jiang, Shanshan Jian, Hui Chen, Tongliang Bu, Zizong Tang, Qingfeng Li, Haixia Zhao, Qi Wu
Summary: Soil salinization is a global problem that affects crop yields and agricultural development. This study investigates the role of auxins and expansins in the salt tolerance of quinoa, a halophyte plant. The results show that auxins contribute to quinoa's salt tolerance by promoting the accumulation of photosynthetic pigments, maintaining antioxidant systems, and scavenging excess reactive oxygen species. The study also identifies genes involved in the salt tolerance regulatory network of quinoa, providing new insights into salt tolerance mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Laura Ravazzolo, Stephanie Boutet-Mercey, Francois Perreau, Cristian Forestan, Serena Varotto, Benedetto Ruperti, Silvia Quaggiotti
Summary: Nitrate regulates root development in maize through the coordinated action of strigolactones (SLs) and auxin. The study found that nitrogen deficiency induces the biosynthesis of zealactone and carlactonoic acid in roots to a greater extent compared to phosphorus deficiency. The research also identified novel components involved in the molecular regulation of maize root response to nitrate.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Plant Sciences
Joyce A. Cartagena, Yao Yao, Shiro Mitsuya, Takashi Tsuge
Summary: Salinity tolerance in rice is influenced by the root's response to salinity stress, with L-type lateral roots showing different sensitivity levels in salt tolerant and sensitive varieties. Nodal roots and S-type lateral roots were negatively affected in both varieties. Gene expression involved in salt tolerance regulation differed between the varieties, with Mulai roots showing more transporter genes and IR29 showing genes associated with transcription regulation. Overall, the identified genes may be beneficial for improving rice varieties with specific root traits for enhanced salinity tolerance.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Plant Sciences
Jiawen Yan, Yu Song, Meng Li, Ting Hu, Yi-Feng Hsu, Min Zheng
Summary: This study identified IRR1 as a key regulator in the formation of adventitious roots in leaf explants. It was found that IRR1 played a role in maintaining ROS homeostasis, and the addition of IAA improved adventitious rooting in irr1 mutants.
PHYSIOLOGIA PLANTARUM
(2023)
Article
Plant Sciences
Tingting Chen, Shijia Lin, Ziping Chen, Tianyuan Yang, Shupei Zhang, Jinsong Zhang, Guohua Xu, Xiaochun Wan, Zhaoliang Zhang
Summary: A study has found that theanine, synthesized by GSI-like proteins in tea plants, plays a crucial role in nitrogen signaling and development. Exogenous theanine inhibits lateral root development by reducing H2O2 accumulation. This study reveals the regulatory role of CsTSI-synthesized theanine in lateral root development in tea plants.
HORTICULTURE RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Bingsheng Lv, Jiayong Zhu, Xiangpei Kong, Zhaojun Ding
Summary: Light serves as the energy source for plant photosynthesis and regulates plant growth and development by controlling auxin biosynthesis and signaling. Recent studies have revealed a new layer of regulation in the IPyA pathway of auxin biosynthesis by light.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Gen Che, Yupeng Pan, Xiaofeng Liu, Min Li, Jianyu Zhao, Shuangshuang Yan, Yuting He, Zhongyi Wang, Zhihua Cheng, Weiyuan Song, Zhaoyang Zhou, Tao Wu, Yiqun Weng, Xiaolan Zhang
Summary: Fruit length is a crucial trait for crop yield and appearance. In this study, a rare allele CsCRCA of the CRABS CLAW gene was identified as a major-effect QTL for fruit size/shape in cucumber. The CsCRCA allele regulates fruit elongation and cell expansion through the regulation of CsARP1 expression.
Article
Hematology
Xia Xiao, Yang Xu, Gillian A. Moschetta, Yang Yu, Allison L. Fisher, Victor M. Alfaro-Magallanes, Shasta McMillen, Sydney Phillips, Chia-Yu Wang, Jan Christian, Jodie L. Babitt
Summary: This study reveals the important role of BMP5 in hepcidin and systemic iron homeostasis regulation, particularly when BMP6 is limited. Bmp5 mutant mice exhibit hepcidin deficiency and iron loading, and loss of one or two functional Bmp5 alleles leads to more severe hemochromatosis in Bmp6 knockout mice. Furthermore, erythroferrone can directly bind to BMP5 and inhibit its induction of hepcidin.
Article
Agronomy
Qianwen Shi, Zuodong Zhou, Zhiwei Hong, Zhi Yang, Zhengquan Gao, Liyun Sun, Jianhua Fan
Summary: The study explains the influence of circadian rhythm and glucose on starch accumulation in Tetraselmis helgolandica var. Tsingtaoensis. Transcriptome analysis reveals the upregulation of certain pathways and genes under circadian rhythm, while glucose inhibits the photosynthetic system. The findings provide insights into starch synthesis in green algae.
GLOBAL CHANGE BIOLOGY BIOENERGY
(2023)
Article
Plant Sciences
Peipei Xu, Hu Jinbo, Weiming Cai
Summary: Shade has a significant impact on various aspects of plant growth and development, such as hypocotyl elongation. This study found that mutations in the KAI2 and MAX2 genes in Arabidopsis led to greater hypocotyl elongation under shade avoidance conditions. This phenotype was caused by the perception of endogenous KAI2-ligands (KLs) and independent of strigolactone biosynthetic or signaling pathways. The study also revealed the involvement of SMAX1 in limiting hypocotyl growth associated with shade avoidance. Overall, the data suggest that KL signaling regulates shade avoidance by modulating auxin homeostasis in the hypocotyl.
Article
Biochemistry & Molecular Biology
Yuxin Liu, Jingbo Zhang, Xinle Li, Liming Zhu, Ziming Lian, Hao Fang, Lu Lu, Ye Lu, Jisen Shi, Jinhui Chen, Zhaodong Hao, Tielong Cheng
Summary: This study identified 12 ARF genes in Nitraria sibirica, a shrub that can survive in extreme drought environments. The ARF genes play important roles in plant growth, development, and stress resistance. Tissue-specific expression patterns and regulatory mechanisms of ARF genes under drought conditions were also investigated.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Dermatology
Rafik Boudra, Yvon Woappi, Diana Wang, Shuyun Xu, Michael Wells, Chrysalyne D. Schmults, Christine G. Lian, Matthew R. Ramsey
Summary: DNA methylation is an important regulatory event that affects gene transcription and physiological processes. This study shows that the levels of 5-hydroxymethylcytosine (5-hmC), an intermediate product in the demethylation cycle, are reduced in cutaneous squamous cell carcinoma tumors. The loss of Tet2 is found to promote the development of squamous cell carcinoma and cooperate with loss of Tp53 to drive tumor formation in epithelial tissues. This study also reveals the role of Tet2 in epidermal lineage specification.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2022)
Article
Plant Sciences
Yusuke Ohba, Sakura Yoshihara, Ryosuke Sato, Keita Matsuoka, Masashi Asahina, Shinobu Satoh, Hiroaki Iwai
Summary: Plants undergo tissue reunion to repair wounds on the stem, and the plant hormone auxin plays a crucial role in this process. A study found that the protein plasmodesmata callose binding protein 2 (PDCB2) affects the expansion of the cambium/phloem region by modulating auxin response during tissue reunion.
JOURNAL OF PLANT RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Jing Wu, Ligeng Ma, Ying Cao
Summary: Precursor message RNA needs processing to produce mature RNA. Cleavage and polyadenylation at the 3'-end in mRNA maturation is a crucial step. The poly(A) tail of mRNA is essential for nuclear export, stability, translation efficiency, and subcellular localization. Most genes have multiple mRNA isoforms through alternative splicing (AS) or alternative polyadenylation (APA), increasing transcriptome and proteome diversity. This review highlights recent advances in APA regulation of gene expression and stress responses in plants, suggesting APA as a novel strategy for plant adaptation to environmental changes and stress responses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agronomy
Namiko Mori, Shota Hasegawa, Ryota Takimoto, Ryo Horiuchi, Chiho Watanabe, Daiki Onizaki, Hayato Shiragane, Atsushi J. Nagano, Elly Kesumawati, Sota Koeda
Summary: In this study, the resistance of a C. chinense accession GR1 against pepper yellow leaf curl Indonesia virus (PepYLCIV) was evaluated. The resistance was found to be controlled by multiple dominant genes. Two novel QTLs associated with PepYLCIV resistance were identified.
Article
Plant Sciences
Kanako Chimura, Shingo Akita, Takaya Iwasaki, Atsushi J. Nagano, Satoshi Shimada
Summary: This study conducted phylogeographic analyses of the Japanese kelp species Eisenia bicyclis. The results showed high genetic differentiation among the Eastern Pacific, Central Pacific, and Sea of Japan coastal regions. Relatively strong gene flow was detected within populations in the Eastern Pacific and in the Sea of Japan. The Central Pacific had high genetic diversity and genetic uniqueness, while the Sea of Japan had low genetic diversity.
JOURNAL OF PHYCOLOGY
(2022)
Article
Developmental Biology
Ji-Seong Kim, Minjeong Jang, Hualin Nie, Jeongeun Lee, Eunhye Hong, Su-Jung Kim, Sun Hyung Kim
Summary: Six novel MADS-box genes were isolated from sweet potato, which were believed to influence the entire root formation. Their expression levels varied at different stages of root development, providing a genetic basis for further research on sweet potato root formation and development.
GENE EXPRESSION PATTERNS
(2022)
Article
Plant Sciences
Yoichi Hashida, Ayumi Tezuka, Yasuyuki Nomura, Mari Kamitani, Makoto Kashima, Yuko Kurita, Atsushi J. Nagano
Summary: This study reveals the differences in transcriptome expression between plants grown in field and controlled environments. The SmartGC growth chamber is capable of reproducing the fluctuating conditions of field environments. The analysis shows that fluctuation of irradiance and temperature affects transcriptome dynamics, while some environmental factors cannot be mimicked by SmartGC.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Plant Sciences
Takanori Kobayashi, Haruka Shinkawa, Atsushi J. Nagano, Naoko K. Nishizawa
Summary: Under low iron availability, plants induce the expression of various genes for iron uptake and translocation. The rice ubiquitin ligases OsHRZ1 and OsHRZ2 repress the expression of these iron-related genes at the transcript level, and the proteins OsGRX6 and OsGRX9 are identified as interacting proteins with OsHRZs. It is also found that the transcription factor OsbZIP83 is preferentially degraded under iron-deficient conditions, and overexpression of OsbZIP83 and OsGRX9 improves rice tolerance to iron deficiency.
Article
Multidisciplinary Sciences
Soichiro Nagano, Naoya Mori, Yukiko Tomari, Noriko Mitsugi, Ayumi Deguchi, Makoto Kashima, Ayumi Tezuka, Atsushi J. Nagano, Hitohide Usami, Takanari Tanabata, Hiroyuki Watanabe
Summary: LED illumination systems, with their low heat emission and high luminous efficiency, have advantages in closed-type plant factories. This study used gene expression analysis to investigate the effects of different light sources on the transcriptome related to leaf aging in leaf lettuce. The results showed that red LED light had the greatest impact on the transcriptome, while blue LED light had less effect. The findings provide valuable information for better growth conditions and efficient green-vegetable production.
Article
Agronomy
Sota Koeda, Namiko Mori, Ryo Horiuchi, Chiho Watanabe, Atsushi J. Nagano, Hayato Shiragane
Summary: In this study, a begomovirus resistance gene named Pepy-2 was identified in pepper, encoding RNA-dependent RNA polymerase 3a. The gene was mapped to chromosome 7 and found to confer resistance against PepYLCIV. This discovery has significant implications for the breeding of begomovirus-resistant peppers.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Plant Sciences
Sujung Kim, Tae Hwa Kim, Mi-Nam Chung, YeongHoon Lee, Im Been Lee, HyeongUn Lee, Won Park
Summary: This study aimed to investigate the effects of microbial communities in cultivated soil on the root rot of sweetpotatoes. The concentrations of Fusarium spp. and microbial communities varied according to the cultivation soil and period. The results provide insights into the importance of cultivating soil and related microorganisms in the advancement of root rot in sweetpotatoes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Noriyuki Onoue, Atsushi Kono, Akifumi Azuma, Ryusuke Matsuzaki, Atsushi J. Nagano, Akihiko Sato
Summary: Inbreeding depression reduces the yield potential of a persimmon population. This study examined the effects of inbreeding on yield-related traits using sequence-based genotyping. The results showed that inbreeding depression occurs in persimmon, and employing an F-M method helps increase the chance of developing high-yielding hybrid cultivars.
Article
Biochemistry & Molecular Biology
Ilham V. Utama, Ixchel F. Mandagi, Sjamsu A. Lawelle, Kawilarang W. A. Masengi, Keiichi Watanabe, Naomi Sawada, Atsushi J. Nagano, Junko Kusumi, Kazunori Yamahira
Summary: Sulawesi is a biodiversity hotspot for ricefishes, and the frequent fragmentation of lakes has contributed to the diversification of these species. In this study, researchers found that both lacustrine and riverine species in the area exhibit significant genetic differentiation, even within a single river system.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Plant Sciences
Bright G. Adu, Aizelle Y. S. Argete, Sakiko Egawa, Atsushi J. Nagano, Akifumi Shimizu, Yoshihiro Ohmori, Toru Fujiwara
Summary: This study describes the isolation and characterization of a introgression line, KRIL37, which carries a small region of the Oryza rufipogon genome in the Oryza sativa L. cv Koshihikari background. KRIL37 was found to have better growth performance and higher capacity for nitrogen uptake and assimilation under low nitrogen conditions. The study suggests the potential to use wild rice genomes to improve modern crops for low nutrient tolerance.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Biochemical Research Methods
Makoto Kashima, Mari Kamitani, Yasuyuki Nomura, Natsumi Mori-Moriyama, Shigeyuki Betsuyaku, Hiromi Hirata, Atsushi J. Nagano
Summary: A novel Direct-RT method was developed for homogenization and direct-lysate reverse transcription of tissue samples without the need for RNA purification. Integration of Direct-RT and targeted RNA-Seq led to the development of a cost-effective, high-throughput quantification method called DeLTa-Seq, which significantly improved the efficiency and accuracy of gene expression analysis. The DeLTa-Seq method demonstrated temperature-dependent effects in Arabidopsis thaliana.
Article
Multidisciplinary Sciences
Yukio Nagano, Hiroaki Tashiro, Sayoko Nishi, Naofumi Hiehata, Atsushi J. Nagano, Shinji Fukuda
Summary: This study analyzed the genetic diversity of loquat and found that many of the internationally collected loquat genetic resources have unknown origins and differ from the genetic background of Japanese and Chinese cultivars. It also discovered that there are loquat varieties with different genetic backgrounds that may have been introduced to Mediterranean countries and North America.
SCIENTIFIC REPORTS
(2022)
Article
Ecology
Satoshi Ansai, Javier Montenegro, Kawilarang W. A. Masengi, Atsushi J. Nagano, Kazunori Yamahira, Jun Kitano
Summary: Recent studies have shown a wide diversity of sex chromosomes in different species. This study investigates the diversity of sex chromosomes in 13 Oryzias species from Sulawesi, Indonesia. Nine of the species were found to have XY systems, with one species possibly having multiple loci involved. Among the seven species that share a sex chromosome linkage group, they vary in the extent of sequence divergence between the X and Y chromosomes. This research highlights the potential for Sulawesian medaka species to be a valuable model system for studying sex chromosome turnover.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Yuichiro Yonetani, Atsushi J. Nagano, Hideki Ueno, Tomoko Amano
Summary: This study examined incubation behavior and egg productivity in hens of a commercial breed in a free-range facility. The results showed that a small percentage of hens exhibited incubation behavior, but their egg productivity was not significantly different from non-incubating hens. The study also compared the incubation behavior and egg productivity of incubating hens with a Silkie Fowl breed hen and found that the Silkie Fowl hen stopped laying after exhibiting incubation behavior, while the incubating hens continued laying eggs. Additionally, a genetic variant associated with incubation behavior was identified through genome-wide association analysis.
JOURNAL OF POULTRY SCIENCE
(2022)