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Involvement of CONSTANS-like Proteins in Plant Flowering and Abiotic Stress Response
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Latest Review Papers in Molecular Plant Sciences 2023

Setsuko Komatsu
1,* and
Andrei Smertenko
Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-0028, Japan
Institute of Biological Chemistry, Washington State University, Washington, WA 99164-7411, USA
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2024, 25(10), 5407;
Submission received: 18 April 2024 / Revised: 4 May 2024 / Accepted: 8 May 2024 / Published: 15 May 2024
(This article belongs to the Special Issue Latest Review Papers in Molecular Plant Sciences 2023)
Success in sustaining food security in the face of global climate change depends on the multi-disciplinary efforts of plant science, physics, mathematics, and computer sciences, whereby each discipline contributes specific concepts, information, and tools. Rapidly accumulating volumes of experimental data about diverse aspects of plant life challenge existing approaches aiming at the interrogation of data and using it to construct models that can predict interactions between genotype and environment. The key role of molecular plant sciences remains to collect reliable information about the fundamental processes of plant biology and organize it in formats that can be used by scientists working in other disciplines. This Special Issue, titled “Latest Review Papers in Molecular Plant Sciences 2023”, aims to collect review papers in all fields of plant sciences. In particular, the aim is to illustrate frontier research in molecular plant science through six review articles covering several important advances in diverse topics. Two articles summarized plant responses to abiotic stress [1,2], two articles addressed responses to biotic stress [3,4], and two articles focused on methodology [5,6].
The erratic weather patterns impose multiple stresses on plants, including a higher content of salts in the soil (salinity), reduced soil moisture content (drought), extremely high day and night temperatures, non-seasonal temperature decreases, and floods [7]. Another consequence of climate change is the spreading of plant pathogens to new geographical locations where previously the weather conditions were suboptimal for the disease. Collectively, the stressful environmental conditions and pathogens can lead to partial or complete yield losses in the affected areas [8]. The yield losses impact food availability, resulting in socio-economic insecurities along with health implications, particularly in marginalized populations [9,10]. Considering the current rate of population growth, sustaining food security requires increasing agricultural output by as much as 50–70% [11]. One of the key contributions of plant molecular biology for sustaining food security focuses on comprehending the impact of abiotic and biotic stress on plants and mechanisms of resiliency to environmental changes.
The introduction of traits associated with greater environmental resiliency into commercial crop varieties using a combination of genomic selection and classical breeding techniques offers an effective strategy for sustaining yields. However, the specificity and sensitivity of phenotyping approaches remain the major bottlenecks for the identification of relevant genetic markers. Advances in omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, paved the way for accelerating the discovery of genetic markers using molecular phenotyping [12,13,14]. Combining multiple omic approaches to a specific experimental condition in the so-called “muti-omics” studies contributes to comprehending the plasticity of metabolic pathways and determining the functions of regulatory genetic networks that control metabolic processes under various environmental conditions in diverse plant species [14,15].
Next-generation sequencing and advanced mass spectrometry enable higher throughput and faster data collection in the multi-omics experiments [16,17], leading to greater accuracy and sensitivity in identifying genetic markers associated with stress resiliency [18]. A complementary technique, organellomics, offers quantitative data on cellular responses under different environmental conditions, hence leading to a deeper comprehension of changes at the molecular level [19]. For example, peroxisome abundance increases in response to heat and drought stress in wheat and quinoa, and peroxisome abundance negatively correlates with yield [20,21]. Pathogens exploit cellular pathways to overcome plant immunity as successful infection with the Wheat Stripe Mosaic Virus was shown to be accompanied by lower peroxisome abundance [22]. Integrating organellomics data and data generated by other techniques with whole-plant phenotyping becomes critical for developing predictive models in plant stress physiology.
Among the most common abiotic stresses, soil salinity is one of the key factors contributing to the decline in crop yields worldwide [23]. The article by Kausar and Komatsu [1] provides an overarching review of morphological, physiological, and molecular responses to salinity stress and relevant tolerance mechanisms in crops. The significance of proteomic approaches for improving salt tolerance of various crops is highlighted, and the contributions of integrated omics approaches to achieving global food security are discussed in the context of previous research findings [24]. Proteomics refers to the study of protein properties, including abundance, post-translational modifications, and protein-protein interactions [25]. For example, proteins related to the reactive-oxygen species scavenging system and abscisic-acid activation are found exclusively in salt-tolerant rice varieties that are capable of accumulating the auxin [26]. The authors propose that novel proteins showing a response to salinity and a correlation with salt stress tolerance are potential candidates for breeding resilient crops.
Another important topic covered in this Special Issue is the relationship between stress and flowering. Regulation of flowering time relies on sensing seasonal changes in the photoperiod [27]. The CONSTANS-like (COL) protein family belongs to the group of photoperiod-sensitive transcription factors with a crucial role in flowering [28]. The article by Zhang et al. [2] highlights recent advances in the characterization of the structure of the COL proteins and their regulatory patterns within transcription complexes. Novel findings about the dual role of COL proteins in flowering and abiotic stress responses provide valuable references for untangling the contribution of COL to stress resilience and exploring the relationship between reproduction and environmental cues.
A major pest of rice, the brown planthopper (BPH), causes significant yield losses in rice [29] by damaging above-ground tissues during the feeding process with piercing-sucking mouthparts. This pathogen is commonly controlled using chemical insecticides [30]. As insecticides affect wildlife, genetic resistance mechanisms are of primary importance. The review by Yan et al. [3] summarized advances in molecular mechanisms for BPH pathogenicity and the breeding of BPH-resistant rice varieties. Genetic analysis led to the identification of 70 genes and a quantitative trait locus (QTL) associated with BPH resistance in rice. However, efficient utilization of these markers required gene/QTL duplication in as many as 26 known cases [31,32,33,34]. The insights from this review could advance the development of sustainable biological control strategies for managing BPH infestations.
L. plantarum is one of the most ubiquitous lactic acid bacteria isolated all over the world from spontaneously fermented plant material [35]. This environmental adaptability highlights the great ecological, technological, and therefore scientific and economic importance of L. plantarum [36]. Skotniczny and Satora [4] provided an overview of molecular techniques, both culture-dependent and culture-independent, currently used to detect and identify L. plantarum. Due to the close relationship between the lactic acid bacteria and L. plantarum species, traditional methods for detection and identification of these species may yield erroneous data. They concluded that quantitative polymerase chain reaction with culture-independent methods provides the most reliable and practical approach for the identification of L. plantarum, whereas commonly used 16S rRNA and shotgun sequencing using next- and third-generation sequencers work better for characterizing the composition of microbial communities than for the identification of single species.
Determining gene functions using genome editing technologies offers a simpler experimental design, higher efficiency, and lower costs in comparison with reverse genetics approaches [37]. However, strong developmental phenotypes or lethality associated with permanent genetic modifications can confound the function and characterization of the genes of interest. More recently, it was reported that fusing the clustered regularly interspaced short palindromic repeats (CRISPR) associated 9 (Cas9) protein with methylation- and histone-modifying enzymes can be used for targeted modulation of the target gene expression by epigenetic mechanisms [38]. Qi et al. [5] summarized the recent progress in epigenome editing by CRISPR-Cas9-related approaches and outlined directions for future development of this technique in plants. They provided examples of how a combination of targeted epigenetic changes and the rapid development of relevant gene editing techniques could be applied to improve important traits in crops.
Endoreplication represents a common modification of the cell cycle in both plants [39] and animals [40] that involves genome replication without subsequent cell division. The final outcome of endoreplication is endopolyploidy. The article by Kołodziejczyk et al. [6] describes the potential of this phenomenon for plant biotechnology. In particular, endopolyploidy can increase the expression of metabolic and stress-tolerance genes [41]. Exploiting the endoreplication in biotechnology and agriculture requires comprehension of approaches for effective and precise induction and sustaining of this process.
Progress in current plant research offers exciting opportunities for advancing tolerance to both biotic and environmental factors by optimizing the expression of functional genes in plants under climate change [42,43,44]. With the rapid innovations in high-throughput technologies, plant stress research begins to tackle the phenomenon of stress memory. The stress memory research is expected to progress from a single-omics level to multi-omics cross-correlation analyses to the systematic construction of the underlying genetic regulatory networks on the scales of molecules, cells, whole plants, and populations. The Editors believe that the review articles published in this Special Issue provide useful information for fundamental research, the development of new applications in plant breeding, and entrepreneurship.

Author Contributions

Conceptualization, S.K.; writing—original draft preparation, S.K.; writing—review and editing, A.S. and S.K. All authors have read and agreed to the published version of the manuscript.


This Editorial received no external funding.

Conflicts of Interest

The authors declare no conflicts of interest.


  1. Kausar, R.; Komatsu, S. Proteomic approaches to uncover salt stress response mechanisms in crops. Int. J. Mol. Sci. 2023, 24, 518. [Google Scholar] [CrossRef] [PubMed]
  2. Zhang, B.; Feng, M.; Zhang, J.; Song, Z. Involvement of CONSTANS-like proteins in plant flowering and abiotic stress response. Int. J. Mol. Sci. 2023, 24, 16585. [Google Scholar] [CrossRef] [PubMed]
  3. Yan, L.; Luo, T.; Huang, D.; Wei, M.; Ma, Z.; Liu, C.; Qin, Y.; Zhou, X.; Lu, Y.; Li, R.; et al. Recent advances in molecular mechanism and breeding utilization of brown planthopper resistance genes in rice: An integrated review. Int. J. Mol. Sci. 2023, 24, 12061. [Google Scholar] [CrossRef] [PubMed]
  4. Skotniczny, M.; Satora, P. Molecular Detection and Identification of Plant-Associated Lactiplantibacillus plantarum. Int. J. Mol. Sci. 2023, 24, 4853. [Google Scholar] [CrossRef] [PubMed]
  5. Qi, Q.; Hu, B.; Jiang, W.; Wang, Y.; Yan, J.; Ma, F.; Guan, Q.; Xu, J. Advances in plant epigenome editing research and its application in plants. Int. J. Mol. Sci. 2023, 24, 3442. [Google Scholar] [CrossRef] [PubMed]
  6. Kołodziejczyk, I.; Tomczyk, P.; Kaźmierczak, A. Endoreplication—Why are we not using its full application potential? Int. J. Mol. Sci. 2023, 24, 11859. [Google Scholar] [CrossRef] [PubMed]
  7. Lesk, C.; Rowhani, P.; Ramankutty, N. Influence of extreme weather disasters on global crop production. Nature 2016, 529, 84–87. [Google Scholar] [CrossRef] [PubMed]
  8. Singh, R.K.; Singh, A.; Zander, K.K.; Mathew, S.; Kumar, A. Measuring successful processes of knowledge co-production for managing climate change and associated environmental stressors: Adaptation policies and practices to support Indian farmers. J. Environ. Manag. 2021, 282, 111679. [Google Scholar] [CrossRef]
  9. Bisoffi, S.; Ahrné, L.; Aschemann-Witzel, J.; Báldi, A.; Cuhls, K.; DeClerck, F.; Duncan, J.; Hansen, H.O.; Hudson, R.L.; Kohl, J.; et al. COVID-19 and sustainable food systems: What should we learn before the next emergency. Front. Sustain. Food Syst. 2021, 5, 650987. [Google Scholar] [CrossRef]
  10. Mishra, A.; Bruno, E.; Zilberman, D. Compound natural and human disasters: Managing drought and COVID-19 to sustain global agriculture and food sectors. Sci. Total Environ. 2021, 754, 142210. [Google Scholar] [CrossRef]
  11. Callegari, A.; Bolognesi, S.; Cecconet, D.; Capodaglio, A.G. Production technologies, current role, and future prospects of biofuels feedstocks: A state-of-the-art review. Crit. Rev. Environ. Sci. Technol. 2020, 50, 384–436. [Google Scholar] [CrossRef]
  12. Mahmood, U.; Li, X.; Fan, Y.; Chang, W.; Niu, Y.; Li, J.; Qu, C.; Lu, K. Multi-omics revolution to promote plant breeding efficiency. Front. Plant Sci. 2022, 13, 1062952. [Google Scholar] [CrossRef] [PubMed]
  13. Muthamilarasan, M.; Singh, N.K.; Prasad, M. Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop species: A climate change perspective. Adv. Genet. 2019, 103, 1–38. [Google Scholar] [CrossRef] [PubMed]
  14. Yang, Y.; Saand, M.A.; Huang, L.; Abdelaal, W.B.; Zhang, J.; Wu, Y.; Li, J.; Sirohi, M.H.; Wang, F. Applications of multi-omics technologies for crop improvement. Front. Plant Sci. 2021, 12, 563953. [Google Scholar] [CrossRef] [PubMed]
  15. Razzaq, A.; Sadia, B.; Raza, A.; Hameed, M.K.; Saleem, F. Metabolomics: A way forward for crop improvement. Metabolites 2019, 9, 303. [Google Scholar] [CrossRef] [PubMed]
  16. Großkinsky, D.K.; Syaifullah, S.J.; Roitsch, T. Integration of multiomics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants. J. Exp. Bot. 2017, 69, 825–844. [Google Scholar] [CrossRef] [PubMed]
  17. Schmidt, J.; Blessing, F.; Fimpler, L.; Wenzel, F. Nanopore sequencing in a clinical routine laboratory: Challenges and opportunities. Clin. Lab. 2020, 66, 1097. [Google Scholar] [CrossRef] [PubMed]
  18. Qi, C.; Jiang, H.; Xiong, J.; Yuan, B.; Feng, Y. On-line trapping/capillary hydrophilic-interaction liquid chromatography/mass spectrometry for sensitive determination of RNA modifications from human blood. Chin. Chem. Lett. 2019, 30, 553–557. [Google Scholar] [CrossRef]
  19. Hickey, K.; Nazarov, T.; Smertenko, A. Organellomic gradients in the fourth dimension. Plant Physiol. 2023, 193, 98–111. [Google Scholar] [CrossRef]
  20. Sanad, M.; Smertenko, A.; Garland-Campbell, K.A. Differential dynamic changes of reduced trait model for analyzing the plastic response to drought phases: A case study in spring wheat. Front. Plant Sci. 2019, 10, 504. [Google Scholar] [CrossRef]
  21. Hinojosa, L.; Sanad, M.N.M.E.; Jarvis, D.E.; Steel, P.; Murphy, K.; Smertenko, A. Impact of heat and drought stress on peroxisome proliferation in quinoa. Plant J. 2019, 99, 1144–1158. [Google Scholar] [CrossRef]
  22. Mishchenko, L.; Nazarov, T.; Dunich, A.; Mishchenko, I.; Ryshchakova, O.; Motsnyi, I.; Dashchenko, A.; Bezkrovna, L.; Fanin, Y.; Molodchenkova, O.; et al. Impact of wheat streak mosaic virus on peroxisome proliferation, redox reactions, and resistance responses in wheat. Int. J. Mol. Sci. 2021, 22, 10218. [Google Scholar] [CrossRef]
  23. Li, X.; Wang, A.; Wan, W.; Luo, X.; Zheng, L.; He, G.; Huang, D.; Chen, W.; Huang, Q. High salinity inhibits soil bacterial community mediating nitrogen cycling. Appl. Environ. Microbiol. 2021, 87, e0136621. [Google Scholar] [CrossRef] [PubMed]
  24. Mansour, M.M.F.; Hassan, F.A.S. How salt stress-responsive proteins regulate plant adaptation to saline conditions. Plant Mol. Biol. 2022, 108, 175–224. [Google Scholar] [CrossRef] [PubMed]
  25. Dai, L.; Li, P.; Li, Q.; Leng, Y.; Zeng, D.; Qian, Q. Integrated multi-omics perspective to strengthen the understanding of salt tolerance in rice. Int. J. Mol. Sci. 2022, 23, 5236. [Google Scholar] [CrossRef]
  26. Saini, S.; Kaur, N.; Marothia, D.; Singh, B.; Singh, V.; Gantet, P.; Pati, P.K. Morphological analysis, protein profiling and expression analysis of auxin homeostasis genes of roots of two contrasting cultivars of rice provide inputs on mechanisms involved in rice adaptation towards salinity stress. Plants 2021, 10, 1544. [Google Scholar] [CrossRef]
  27. Jackson, S.D. Plant responses to photoperiod. New Phytol. 2009, 181, 517–531. [Google Scholar] [CrossRef] [PubMed]
  28. Shim, J.S.; Imaizumi, T. Circadian clock and photoperiodic response in Arabidopsis: From seasonal flowering to redox homeostasis. Biochemistry 2015, 54, 157–170. [Google Scholar] [CrossRef]
  29. Savary, S.; Willocquet, L.; Pethybridge, S.J.; Esker, P.; McRoberts, N.; Nelson, A. The global burden of pathogens and pests on major food crops. Nat. Ecol. Evol. 2019, 3, 430–439. [Google Scholar] [CrossRef]
  30. Lu, K.; Chen, X.; Liu, W.; Zhang, Z.; Wang, Y.; You, K.; Li, Y.; Zhang, R.; Zhou, Q. Characterization of heat shock protein 70 transcript from Nilaparvata lugens Stål: Its response to temperature and insecticide stresses. Pestic. Biochem. Phys. 2017, 142, 102–110. [Google Scholar] [CrossRef]
  31. Yang, M.; Cheng, L.; Yan, L.; Shu, W.; Wang, X.; Qiu, Y. Mapping and characterization of a quantitative trait locus resistance to the brown planthopper in the rice variety IR64. Hereditas 2019, 156, 22. [Google Scholar] [CrossRef] [PubMed]
  32. Zhou, C.; Zhang, Q.; Chen, Y.; Huang, J.; Guo, Q.; Li, Y.; Wang, W.; Qiu, Y.; Guan, W.; Zhang, J.; et al. Balancing selection and wild gene pool contribute to resistance in global rice germplasm against planthopper. J. Integr. Plant Biol. 2021, 63, 1695–1711. [Google Scholar] [CrossRef] [PubMed]
  33. Tan, H.Q.; Palyam, S.; Gouda, J.; Kumar, P.P.; Chellian, S.K. Identification of two QTLs, Bph41 and Bph42, and their respective gene candidates for brown planthopper resistance in rice. Sci. Rep. 2022, 12, 18538. [Google Scholar] [CrossRef] [PubMed]
  34. Wang, X.; Han, Y.; Zhang, Y.; Deng, B.; Wu, B.; Guo, X.; Qin, Y.; Fang, Y.; Liu, F.; Qin, B.; et al. QTL mapping integrated with BSA-seq analysis identifies a novel gene conferring resistance to brown planthopper from common wild rice (Oryza rufipogon griff.). Euphytica 2022, 218, 34. [Google Scholar] [CrossRef]
  35. Maidana, S.D.; Ficoseco, C.A.; Bassi, D.; Cocconcelli, P.S.; Puglisi, E.; Savoy, G.; Vignolo, G.; Fontana, C. Biodiversity and technological-functional potential of lactic acid bacteria isolated from spontaneously fermented chia sourdough. Int. J. Food Microbiol. 2020, 316, 108425. [Google Scholar]
  36. Wang, Z.; Chao, Y.; Deng, Y.; Piao, M.; Chen, T.; Xu, J.; Zhang, R.; Zhao, J.; Deng, Y. Formation of viable, but putatively non-culturable (VPNC) cells of beer-spoilage lactobacilli growing in biofilms. LWT 2020, 133, 109964. [Google Scholar] [CrossRef]
  37. Samanta, M.K.; Dey, A.; Gayen, S. CRISPR/Cas9: An advanced tool for editing plant genomes. Transgenic Res. 2016, 25, 561–573. [Google Scholar] [CrossRef] [PubMed]
  38. Molla, K.A.; Sretenovic, S.; Bansal, K.C.; Qi, Y. Precise plant genome editing using base editors and prime editors. Nat. Plants 2021, 7, 1166–1187. [Google Scholar] [CrossRef] [PubMed]
  39. Lee, H.O.; Davidson, J.M.; Duronio, R.J. Endoreplication: Polyploidy with purpose. Genes Dev. 2009, 23, 2461–2477. [Google Scholar] [CrossRef]
  40. Meng, X.; Dang, H.Q.; Kapler, G.M. Developmentally programmed switches in DNA replication: Gene amplification and genome-wide endoreplication in Tetrahymena. Microorganisms 2023, 11, 491. [Google Scholar] [CrossRef]
  41. Yoshiyama, K.O. SOG1: A master regulator of the DNA damage response in plants. Genes Genet. Syst. 2015, 90, 209–216. [Google Scholar] [CrossRef] [PubMed]
  42. Bailey-Serres, J.; Parker, J.E.; Ainsworth, E.A.; Oldroyd, G.E.D.; Schroeder, J.I. Genetic strategies for improving crop yields. Nature 2019, 575, 109–118. [Google Scholar] [CrossRef] [PubMed]
  43. Fróna, D.; Szenderák, J.; Harangi-Rákos, M. The challenge of feeding the world. Sustainability 2019, 11, 5816. [Google Scholar] [CrossRef]
  44. Pandey, D. Agricultural sustainability and climate change nexus. In Contemporary Environmental Issues and Challenges in Era of Climate Change; Singh, P., Singh, R.P., Srivastava, V., Eds.; Springer: Singapore, 2020; pp. 77–97. [Google Scholar]
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Komatsu, S.; Smertenko, A. Latest Review Papers in Molecular Plant Sciences 2023. Int. J. Mol. Sci. 2024, 25, 5407.

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Komatsu S, Smertenko A. Latest Review Papers in Molecular Plant Sciences 2023. International Journal of Molecular Sciences. 2024; 25(10):5407.

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Komatsu, Setsuko, and Andrei Smertenko. 2024. "Latest Review Papers in Molecular Plant Sciences 2023" International Journal of Molecular Sciences 25, no. 10: 5407.

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