Abstract Mollusca is the largest marine phylum, comprising about 23% of all named marine organisms, Mollusca systematics are still in flux, and an increase in human activities has affected Molluscan reproduction and development, strongly impacting diversity and classification. Therefore, it is necessary to explore the mitochondrial genome of Mollusca. The Mollusca mitochondrial database (MODB) was established for the Life and Health Big Data Center of Yantai University. This database is dedicated to collecting, sorting and sharing basic information regarding mollusks, especially their mitochondrial genome information. We also integrated a series of analysis and visualization tools, such as BLAST, MUSCLE, GENEWISE and LASTZ. In particular, a phylogenetic tree was implemented in this database to visualize the evolutionary relationships between species. The original version contains 616 species whose mitochondrial genomes have been sequenced. The database provides comprehensive information and analysis platform for researchers interested in understanding the biological characteristics of mollusks. Database URL: http://modb.ytu.edu.cn/
In contrast to obligate bacteria, facultative symbiotic bacteria are mainly characterized by genome enlargement. However, the underlying relationship of this feature with adaptations to various habitats remains unclear. In this study, we used the global genome data of Nostoc strains, including 10 novel genomes sequenced in this study and 26 genomes available from public databases, and analyzed their evolutionary history. The evolutionary boundary of the real clade of Nostoc species was identified and was found to be consistent with the results of polyphasic taxonomy. The initial ancestral species of Nostoc was demonstrated to be consistent with a facultative symbiotic population. Further analyses revealed that Nostoc strains tended to shift from facultative symbiosis to a free-living one, along with an increase in genome sizes during the dispersal of each exterior branch. Intracellular symbiosis was proved to be essentially related to Nostoc evolution, and the adaptation of its members to free-living environments was coupled with a large preference for gene acquisition involved in gene repair and recombination. These findings provided unique evidence of genomic mechanisms by which homologous microbes adapt to distinct life manners and external environments.
Bio-manufacturing via microbial cell factory requires large promoter library for fine-tuned metabolic engineering. Ogataea polymorpha, one of the methylotrophic yeasts, possesses advantages in broad substrate spectrum, thermal-tolerance, and capacity to achieve high-density fermentation. However, a limited number of available promoters hinders the engineering of O. polymorpha for bio-productions. Here, we systematically characterized native promoters in O. polymorpha by both GFP fluorescence and fatty alcohol biosynthesis. Ten constitutive promoters (P PDH , P PYK , P FBA , P PGM , P GLK , P TRI , P GPI , P ADH1 , P TEF1 and P GCW14 ) were obtained with the activity range of 13%-130% of the common promoter P GAP (the promoter of glyceraldehyde-3-phosphate dehydrogenase), among which P PDH and P GCW14 were further verified by biosynthesis of fatty alcohol. Furthermore, the inducible promoters, including ethanol-induced P ICL1 , rhamnose-induced P LRA3 and P LRA4 , and a bidirectional promoter (P Mal -P Per ) that is strongly induced by sucrose, further expanded the promoter toolbox in O. polymorpha. Finally, a series of hybrid promoters were constructed via engineering upstream activation sequence (UAS), which increased the activity of native promoter P LRA3 by 4.7-10.4 times without obvious leakage expression. Therefore, this study provided a group of constitutive, inducible, and hybrid promoters for metabolic engineering of O. polymorpha, and also a feasible strategy for rationally regulating the promoter strength.
This commentary on Zeng et al. (2025, Cell) discusses the role of COOL1 in maize cold adaptation, highlighting its significance for high-latitude adaptation and the potential for molecular design breeding to enhance cold tolerance in maize. In the face of accelerating global climate change, developing crops that can withstand extreme environmental conditions, such as cold temperatures at high latitudes, has become a critical challenge for ensuring global food security. In addition, as the population increases, it is essential to expand planting areas to northern regions with lower accumulated yearly temperatures. Natural variations of crops are artificially selected to adapt to extreme temperature environments during their domestication. For the temperate crops like maize and rice, striking a trade-off between growth development and cold tolerance is essential for breeding. Investigating the functional mechanisms of gene modules related to high-latitude and high-altitude adaptation shaped by natural selection, offers great potential to improve cold resilience in elite varieties. The recent paper by Zeng et al. (2025), published in Cell, provides a significant breakthrough in understanding maize (Zea mays) adaptation to cold stress, particularly its evolution and genetic mechanisms for tolerance in high-latitude regions. The findings by Zeng et al. provide valuable insights that not only advance the molecular understanding of cold tolerance in maize but also open up exciting prospects for breeding cold-tolerant maize varieties for future climate challenges. Studies on cold sensing and signaling transduction network are well-established in plants, which provides critical insights into cold tolerance and potential molecular breeding targets (Yang et al., 2023). However, the knowledge on cold adaptation in most crops remains limited. In rice, the signaling network for chilling tolerance from the sensors to the downstream factors has been well established, and several genes have been identified as key players in cold adaptation which are potential targets for molecular design breeding. For example, COLD1 acts as a cold sensor to mediate cold-induced calcium influx. A specific variant, COLD1SNP2, derived from the Chinese population of Oryza rufipogon, confers chilling tolerance and facilitates adaptation to colder environments. The COLD1 module has been incorporated into the designed national variety Jiaheyou 7. Another example is COLD6, which forms a complex with OSMOTIN-LIKE 1 (OSM1) to elevate 2ʹ,3ʹ-cAMP levels and enhance chilling tolerance. The COLD6jap allele, which spread across northern regions of China, Japan, Korea, and parts of Europe, has been instrumental in rice northern expansion. The COLD6jap allele has shown a great potential to improve cold resilience in three-line hybrid rice (Guo et al., 2024). Moreover, an oxygen-sensing mechanism for angiosperm adaptation to altitude has been revealed (Abbas et al., 2022). Similarly, studies on Tibetan semi-wild wheat have highlighted how genomic reshaping in response to high altitudes enables adaptation through specific genomic regions (Guo et al., 2020). These discoveries underscore the importance of cold-tolerant genes in enabling crop adaptation to cold environments and provide valuable molecular targets for improving cold resilience in crops. Maize (Zea mays), a major food crop contributing approximately 40% of global cereal production (FAO, http://faostat.fao.org/), faces increasing challenges from cold stress in high-latitude regions. Originating from its wild relative, teosinte, in southern Mexico about 9,000 years ago (Matsuoka et al., 2002), maize spread rapidly to temperate regions prior to the discovery of the Americas by Columbus. Nowadays, its cultivation spans a broad latitudinal range, from 40°S to 58°N, with temperate regions accounting for approximately 80% of global production. Maize expansion from tropical to temperate regions requires a reduction in its sensitivity to photoperiod in order to adapt to long-day conditions (Liang et al., 2021). Meanwhile, maize had to develop the ability to cope with the low temperatures at higher latitudes and altitudes. Over the years, several key genes responsible for maize flowering adaptability have been identified, such as CONSTANS, CONSTANS-LIKE, TOC1 (CCT) genes CCT9 and CCT10, Zea CENTRORADIALIS 8 (ZCN8), FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1), and MADS69 (Liang et al., 2021; Zhao et al., 2023; Chen et al., 2024). In terms of cold tolerance, several genes such as ZmRR1, bZIP68, ICE1, and HSF21 have also been identified as key regulators of cold tolerance in maize (Yang et al., 2023; Gao et al., 2024). Despite these progresses, a comprehensive understanding of the molecular genetic mechanisms underlying the adaptation of high-latitude cold climates in maize remain largely unexplored. In their paper, Zeng et al. (2025) highlight a major advance in understanding maize cold tolerance, especially its adaptation to high latitudes. The authors investigated the genetic basis of seedling-stage cold tolerance using a diverse panel of 205 inbred maize lines, including 88 tropical/subtropical, 75 temperate, and 42 mixed types, through genome-wide association studies (GWAS). This led to the identification of COOL1 (COLD-RESPONSIVE OPERATION LOCUS 1), a key gene in regulating cold tolerance. The near-isogenic lines, clustered regularly interspaced small palindromic repeats (CRISPR)/CRISPR-associated protein 9 knockout lines and COOL1 overexpression plants demonstrated that COOL1 functions as a negative regulator of cold tolerance in maize. A deeper analysis revealed that nine single nucleotide polymorphisms (SNPs) in the COOL1 promoter region are significantly associated with gene expression levels and cold tolerance. Notably, four of the most significant SNPs are in complete linkage disequilibrium and reside within an A-box motif. To further dissect how COOL1 regulates cold tolerance, the authors employed a combination of molecular and biochemical assays, including chromatin immunoprecipitation – polymerase chain reaction (ChIP-PCR), electrophoretic mobility shift assay, and transient dual-luciferase (LUC) assays. Their results revealed that the bZIP transcription factor ELONGATED HYPOCOTYL5 (HY5), a positive regulator of cold tolerance, suppresses the transcription of COOL1 gene by directly binding to the A box motif in its promoter region of the COOL1HapA allele. In contrast, the cold sensitive COOL1HapB allele shows minimal binding affinity for HY5, leading to increased COOL1 gene expression. Further RNA sequencing and ChIP-sequencing (ChIP-seq) analyses demonstrated that COOL1 directly targets a subset of DREB1 genes, which encode key transcription factors involved in cold tolerance, as well as TREHALOSE-6-PHOSPHATE SYNTHASE (TPS) genes which are involved in the biosynthesis of the osmolyte trehalose. COOL1 negatively regulates the expression of both gene sets. It will be interesting to address the physiological function of the negative regulation in future studies. Additionally, the data showed that low temperatures led the translocation of protein kinase CPK17 into the nucleus, where it phosphorylates COOL1, enhancing its protein stability and further promoting the negative regulation of cold tolerance. This intricate molecular mechanism involving both transcriptional and post-translational regulation provides a deeper understanding of how maize responds to low temperatures. One of the most striking findings of this study is the identification of a strong association between the COOL1 alleles and maize's geographic distribution. Zeng et al. genotyped the COOL1 alleles in 1,008 maize landrace accessions, which represent the entire pre-Columbian range of maize landraces across the Americas. They showed that the cold-tolerant COOL1HapA allele is predominant in high-latitude regions, while the cold-sensitive COOL1HapB allele is more common in warmer areas at lower latitudes. As latitude increases, the frequency of the cold-tolerant COOL1HapA allele sharply rises, ultimately becoming nearly fixed in the United States. This observation supports the hypothesis that COOL1 has been shaped by natural selection in response to cold climates, particularly in northern environments where maize has expanded its range over the centuries. The fact that the cold-tolerant COOL1HapA allele variant is present in over half of the examined teosinte lines suggests that this allele predates the domestication of maize, further emphasizing its evolutionary significance (Figure 1). Moreover, analysis of major cultivated varieties in China, such as Xianyu 335, Zhengdan 958, showed that some parents carry the cold-sensitive COOL1HapB allele, suggesting the significant potential for improving cold tolerance by incorporating favorable COOL1 alleles into breeding programs. Notably, the COOL1 mutation confers cold tolerance without compromising yield potential under non-stressful conditions, making the COOL1HapA allele a promising candidate for breeding cold-tolerant maize varieties. This insight opens up exciting possibilities for developing maize varieties that can thrive in high-latitude regions or other areas subject to unpredictable cold snaps. Taken together, the discoveries made by Zeng et al. (2025) provide essential gene resources and molecular targets for improving cold resilience in maize. Moving forward, breeding strategies should focus on pyramiding multiple cold-tolerant alleles, including those of COOL1, to develop "super cold-resilient" maize varieties. Meanwhile, it is crucial to trade off between cold tolerance with other important agronomic traits, such as yield potential, disease resistance, and drought tolerance. As global climate change continues, integrating cold tolerance with these other traits will be essential for developing varieties that can thrive in diverse and increasingly challenging environments. It may provide a potential strategy example to improve the resilience trait in molecular design for breeding using the COOL1 allele. The COOL1HapA is adapted to higher latitudes with lower temperatures in maize Proportional distribution of the two haplotypes (HapA and HapB) in 1,008 maize landraces from different latitudinal regions of the Americas. COOL1HapA, a cold-tolerant allele, is present at a relatively higher proportion in high-latitude, cooler regions, while the cold-sensitive COOL1HapB allele predominates in warmer areas at lower-latitude. Under cold stress, HY5 binds more effectively to the COOL1HapA promoter due to natural variations in the A-box (TACGTA), reducing COOL1 expression and enhancing cold tolerance in COOL1HapA lines. The differential HY5 binding affinities lead to varying COOL1 transcription and translation levels, affecting the activation of cold-responsive genes. Additionally, COOL1 phosphorylation by CPK17 enhances its stability and function. We sincerely thank the Young Scientists Fund of the National Natural Science Foundation of China (Grant No. 32200244) and the National Key Research and Development Program of China (Grant No. 2020YFA0509901-1) for financial support. The authors declare no conflict of interest. Xiaoyu Guo and Kang Chong conceptualized the manuscript. Xiaoyu Guo drafted the manuscript and prepared the figure. Kang Chong revised the manuscript. All authors read and approved the final manuscript.
This work characterized a novel endotype xanthanase, MiXen, and elucidated that the C-terminal carbohydrate-binding module of MiXen could drastically enhance the hydrolysis activity of the enzyme toward highly ordered xanthan. Both the sequence and structural analysis demonstrated that the catalytic domain and carbohydrate-binding module of MiXen belong to the novel branch of the GH9 family and CBMs, respectively. This xanthan cleaver can help further reveal the enzymolysis mechanism of xanthan and provide an efficient tool for the production of molecular modified xanthan with new physicochemical and physiological functions.
Calcineurin B-like interacting protein kinases (CIPKs) play important roles via environmental stress. However, less is known how to sense the stress in molecular structure conformation level. Here, an OsCIPK7 mutant via TILLING procedure with a point mutation in the kinase domain showed increased chilling tolerance, which could be potentially used in the molecular breeding. We found that this point mutation of OsCIPK7 led to a conformational change in the activation loop of the kinase domain, subsequently with an increase of protein kinase activity, thus conferred an increased tolerance to chilling stress.
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