5.9
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5.9
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2021 Vol. 48, No. 11

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Review
Nucleolus-localized Def-CAPN3 protein degradation pathway and its role in cell cycle control and ribosome biogenesis
Shuyi Zhao, Delai Huang, Jinrong Peng
2021, 48(11): 955-960. doi: 10.1016/j.jgg.2021.06.011
Abstract (232) HTML PDF (47)
Abstract:
The nucleolus, as the ‘nucleus of the nucleus’, is a prominent subcellular organelle in a eukaryocyte. The nucleolus serves as the centre for ribosome biogenesis, as well as an important site for cell-cycle regulation, cellular senescence, and stress response. The protein composition of the nucleolus changes dynamically through protein turnover to meet the needs of cellular activities or stress responses. Recent studies have identified a nucleolus-localized protein degradation pathway in zebrafish and humans, namely the Def-CAPN3 pathway, which is essential to ribosome production and cell-cycle progression, by controlling the turnover of multiple substrates (e.g., ribosomal small-subunit[SSU] processome component Mpp10, transcription factor p53, check-point proteins Chk1 and Wee1). This pathway relies on the Ca2+-dependent cysteine proteinase CAPN3 and is independent of the ubiquitin-mediated proteasome pathway. CAPN3 is recruited by nucleolar protein Def from cytoplasm to nucleolus, where it proteolyzes its substrates which harbor a CAPN3 recognition-motif. Def depletion leads to the exclusion of CAPN3 and accumulation of p53, Wee1, Chk1, and Mpp10 in the nucleolus that result in cell-cycle arrest and rRNA processing abnormality. Here, we summarize the discovery of the Def-CAPN3 pathway and propose its biological role in cell-cycle control and ribosome biogenesis.
Original research
TEAseq-based identification of 35,696 Dissociation insertional mutations facilitates functional genomic studies in maize
Mingjie Lyu, Huafeng Liu, Joram Kiriga Waititu, Ying Sun, Huan Wang, Junjie Fu, Yanhui Chen, Jun Liu, Lixia Ku, Xiliu Cheng
2021, 48(11): 961-971. doi: 10.1016/j.jgg.2021.07.010
Abstract (260) PDF (28)
Abstract:
In plants, transposable element (TE)-triggered mutants are important resources for functional genomic studies. However, conventional approaches for genome-wide identification of TE insertion sites are costly and laborious. This study developed a novel, rapid, and high-throughput TE insertion site identification workflow based on next-generation sequencing and named it Transposable Element Amplicon Sequencing (TEAseq). Using TEAseq, we systemically profiled the Dissociation (Ds) insertion sites in 1606 independent Ds insertional mutants in advanced backcross generation using K17 as background. The Ac-containing individuals were excluded for getting rid of the potential somatic insertions. We characterized 35,696 germinal Ds insertions tagging 10,323 genes, representing approximately 23.3% of the total genes in the maize genome. The insertion sites were presented in chromosomal hotspots around the ancestral Ds loci, and insertions occurred preferentially in gene body regions. Furthermore, we mapped a loss-of-function AGL2 gene using bulked segregant RNA-sequencing assay and proved that AGL2 is essential for seed development. We additionally established an open-access database named MEILAM for easy access to Ds insertional mutations. Overall, our results have provided an efficient workflow for TE insertion identification and rich sequence-indexed mutant resources for maize functional genomic studies.
Micro-coevolution of host genetics with gut microbiome in three Chinese ethnic groups
Mingyue Cheng, Xueling Ge, Chaofang Zhong, Ruiqing Fu, Kang Ning, Shuhua Xu
2021, 48(11): 972-983. doi: 10.1016/j.jgg.2021.09.002
Abstract (394) PDF (58)
Abstract:
Understanding the micro-coevolution of the human gut microbiome with host genetics is challenging but essential in both evolutionary and medical studies. To gain insight into the interactions between host genetic variation and the gut microbiome, we analyzed both the human genome and gut microbiome collected from a cohort of 190 students in the same boarding college and representing 3 ethnic groups, Uyghur, Kazakh, and Han Chinese. We found that differences in gut microbiome were greater between genetically distinct ethnic groups than those genetically closely related ones in taxonomic composition, functional composition, enterotype stratification, and microbiome genetic differentiation. We also observed considerable correlations between host genetic variants and the abundance of a subset of gut microbial species. Notably, interactions between gut microbiome species and host genetic variants might have coordinated effects on specific human phenotypes. Bacteroides ovatus, previously reported to modulate intestinal immunity, is significantly correlated with the host genetic variant rs12899811 (meta-P=5.55 × 10-5), which regulates the VPS33B expression in the colon, acting as a tumor suppressor of colorectal cancer. These results advance our understanding of the micro-coevolution of the human gut microbiome and their interactive effects with host genetic variation on phenotypic diversity.
Cochlear hair cells of echolocating bats are immune to intense noise
Zhen Liu, Peng Chen, Yuan-Yuan Li, Meng-Wen Li, Qi Liu, Wen-Lu Pan, Dong-Ming Xu, Jing Bai, Li-Biao Zhang, Jie Tang, Peng Shi
2021, 48(11): 984-993. doi: 10.1016/j.jgg.2021.06.007
Abstract (200) HTML PDF (35)
Abstract:
Exposure to intense noise can damage cochlear hair cells, leading to hearing loss in mammals. To avoid this constraint, most mammals have evolved in relatively quiet environments. Echolocating bats, however, are naturally exposed to continuous intense sounds from their own and neighboring sonar emissions for maintaining sonar directionality and range. Here, we propose the presence of intense noise resistance in cochlear hair cells of echolocating bats against noise-induced hearing loss (NIHL). To test this hypothesis, we performed noise exposure experiments for laboratory mice, one nonecholocating bat species, and five echolocating bat species. Contrary to nonecholocating fruit bats and mice, the hearing and the cochlear hair cells of echolocating bats remained unimpaired after continuous intense noise exposure. The comparative analyses of cochleae transcriptomic data showed that several genes protecting cochlear hair cells from intense sounds were overexpressed in echolocating bats. Particularly, the experimental examinations revealed that ISL1 overexpression significantly improved the survival of cochlear hair cells. Our findings support the existence of protective effects in cochlear hair cells of echolocating bats against intense noises, which provides new insight into understanding the relationship between cochlear hair cells and intense noises, and preventing or ameliorating NIHL in mammals.
Genetic diversity and population structure of Leptosphaeria maculans isolates in Western Canada
Qilin Chen, Gary Peng, Randy Kutcher, Fengqun Yu
2021, 48(11): 994-1006. doi: 10.1016/j.jgg.2021.06.019
Abstract (177) PDF (27)
Abstract:
Leptosphaeria maculans is a serious concern for canola production worldwide. For effective disease management, knowledge of the pathogen's genetic variability and population structure is a prerequisite. In this study, whole-genome sequencing was performed for 162 of 1590 L. maculans isolates collected in the years 2007-2008 and 2012-2014 in Western Canada. DNA variants in genome-wide and specific regions including avirulence (Avr) genes were characterized. A total of 31,870 high-quality polymorphic DNA variants were used to study L. maculans genetic diversity and population structure. Cluster analysis showed that 150 isolates were clustered into 2 main groups and 4 subgroups by DNA variants located in either Avr or small secreted protein-encoding genes and into 2 main groups and 6 subgroups by genome-wide variants. The analysis of nucleotide diversity and differentiation also confirmed genetic variation within a population and among populations. Principal component analysis with genome-wide variants showed that the isolates collected in 2012-2014 were more genetically diverse than those collected in 2007-2008. Population structure analysis discovered three distinct sub-populations. Although isolates from Saskatchewan and Alberta were of similar genetic composition, Manitoba isolates were highly diverse. Genome-wide association study detected DNA variants in genes AvrLm4-7, Lema_T86300, and Lema_T86310 associated with the years of collection.
A hypothetical model of trans-acting R-loops-mediated promoter-enhancer interactions by Alu elements
Xue Bai, Feifei Li, Zhihua Zhang
2021, 48(11): 1007-1019. doi: 10.1016/j.jgg.2021.07.005
Abstract (237) PDF (30)
Abstract:
Enhancers modulate gene expression by interacting with promoters. Models of enhancer-promoter interactions (EPIs) in the literature involve the activity of many components, including transcription factors and nucleic acid. However, the role that sequence similarity plays in EPIs remains largely unexplored. Herein, we report that Alu-derived sequences dominate sequence similarity between enhancers and promoters. After rejecting alternative DNA:DNA and DNA:RNA triplex models, we propose that enhancer-associated RNAs (eRNAs) may directly contact their targeted promoters by forming trans-acting R-loops at those Alu sequences. We show how the characteristic distribution of functional genomic data, such as RNA-DNA proximate ligation reads, binding of transcription factors, and RNA-binding proteins, all align with the Alu sequences of EPIs. We also show that these aligned Alu sequences may be subject to the constraint of coevolution, further implying the functional significance of these R-loop hybrids. Finally, our results imply that eRNA and Alu elements associate in a manner previously unrecognized in EPIs and the evolution of gene regulation networks in mammals.
Mycobacterium Lrp/AsnC family transcriptional factor modulates the arginase pathway as both a sensor and a transcriptional repressor
Shuangquan Yan, Junfeng Zhen, Yuzhu Li, Yu Huang, Xuefeng Ai, Yue Li, Andrea Stojkoska, Xue Huang, Cao Ruan, Jiang Li, Lin Fan, Jianping Xie
2021, 48(11): 1020-1031. doi: 10.1016/j.jgg.2021.06.018
Abstract (138) PDF (12)
Abstract:
L-Arginine is the precursor of nitric oxide (NO), a host immune effector against intracellular pathogens including Mycobacterium tuberculosis (M. tb). Pathogens including M. tb have evolved various strategies targeting arginine to block the production of NO for better survival and proliferation. However, L-arginine metabolism and regulation in Mycobacterium are poorly understood. Here, we report the identification of M. smegmatis MSMEG_1415 (homolog of M. tb Rv2324) as an arginine-responsive transcriptional factor regulating the arginase pathway. In the absence of L-arginine, MSMEG_1415 acts as a repressor to inhibit the transcription of the roc (for arginine, ornithine catabolism) gene cluster, thereby switching off the arginase pathway. Treatment with L-arginine relieves the transcriptional inhibition of MSMEG_1415 on the roc gene cluster to activate the arginase pathway. Moreover, the L-arginine-MSMEG_1415 complex activates the transcription of the roc gene cluster by recognizing and binding a 15-bp palindrome motif, thereby preventing the excess accumulation of L-arginine in M. smegmatis. Physiologically, MSMEG_1415 confers mycobacteria resistance to starvation and fluoroquinolones exposure, suggestive of its important role in M. smegmatis persistence. The results uncover a unique regulatory mechanism of arginine metabolism in mycobacteria and identify M. tb Rv2324 as an attractive candidate target for the design of drugs against tuberculosis.
Letter to the editor
The HuaBiao project: whole-exome sequencing of 5000 Han Chinese individuals
Meng Hao, Weilin Pu, Yi Li, Shaoqing Wen, Chang Sun, Yanyun Ma, Hongxiang Zheng, Xingdong Chen, Jingze Tan, Guoqing Zhang, Menghan Zhang, Shuhua Xu, Yi Wang, Hui Li, Jiucun Wang, Li Jin
2021, 48(11): 1032-1035. doi: 10.1016/j.jgg.2021.07.013
Abstract (685) PDF (144)
Abstract:
Establishment of transposase-assisted low-input m6A sequencing technique
Tao Chen, Yan Li, Dong-Zhao Ma, Zhang Zhang, Jian-Fei Xi, Guan-Zheng Luo
2021, 48(11): 1036-1039. doi: 10.1016/j.jgg.2021.08.007
Abstract (567) PDF (117)
Abstract:
A backbone parent contributes core genomic architecture to pedigree breeding of early-season indica rice
Junyu Chen, Huali Zhang, Shuhan Deng, Huilong Du, Zhuo Chen, Yuhui Zhao, Dongqing Dai, Chengzhen Liang, Ximing Li, Chengzhi Liang, Rui Zhang, Liangyong Ma
2021, 48(11): 1040-1043. doi: 10.1016/j.jgg.2021.07.011
Abstract (208) PDF (33)
Abstract: