@article{mateos_picln_2022,
	title = {{PICLN} modulates alternative splicing and light/temperature responses in plants},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac527},
	doi = {10.1093/plphys/kiac527},
	abstract = {Plants undergo transcriptome reprogramming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the methylosome complex. Ion Chloride nucleotide-sensitive protein (PICLN) is part of the methylosome complex in both humans and Arabidopsis (Arabidopsis thaliana), and we show here that the human PICLN ortholog rescues phenotypes of Arabidopsis picln mutants. Altered photomorphogenic and photoperiodic responses in Arabidopsis picln mutants are associated with changes in pre-mRNA splicing that partially overlap with those in PROTEIN-ARGININE METHYL TRANSFERASE5 (prmt5) mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PRMT5, the main protein of the methylosome, are controlled by Arabidopsis GEMIN2. As with GEMIN2 and SM PROTEIN E1/PORCUPINE (SME1/PCP), low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.},
	urldate = {2022-12-02},
	journal = {Plant Physiology},
	author = {Mateos, Julieta L and Sanchez, Sabrina E and Legris, Martina and Esteve-Bruna, David and Torchio, Jeanette C and Petrillo, Ezequiel and Goretti, Daniela and Blanco-Touriñán, Noel and Seymour, Danelle K and Schmid, Markus and Weigel, Detlef and Alabadí, David and Yanovsky, Marcelo J},
	month = nov,
	year = {2022},
	pages = {kiac527},
}

Plants undergo transcriptome reprogramming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the methylosome complex. Ion Chloride nucleotide-sensitive protein (PICLN) is part of the methylosome complex in both humans and Arabidopsis (Arabidopsis thaliana), and we show here that the human PICLN ortholog rescues phenotypes of Arabidopsis picln mutants. Altered photomorphogenic and photoperiodic responses in Arabidopsis picln mutants are associated with changes in pre-mRNA splicing that partially overlap with those in PROTEIN-ARGININE METHYL TRANSFERASE5 (prmt5) mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PRMT5, the main protein of the methylosome, are controlled by Arabidopsis GEMIN2. As with GEMIN2 and SM PROTEIN E1/PORCUPINE (SME1/PCP), low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.

@article{aghbolaghi_stipagrostis_2022,
	title = {Stipagrostis pennata ({Trin}.) {De} {Winter} {Artificial} {Seed} {Production} and {Seedlings} {Multiplication} in {Temporary} {Immersion} {Bioreactors}},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/11/22/3122},
	doi = {10.3390/plants11223122},
	abstract = {This study was conducted to develop the protocol for artificial seed production of Stipagrostis pennata (Trin.) De Winter via somatic embryo encapsulation as well as test a temporary bioreactor system for germination and seedling growth. Embryogenic calli were encapsulated using sodium alginate and calcium chloride and then sowed in the Murashige and Skoog (MS) germination medium in in vitro cultures. The experiments were conducted as a factorial based on a completely randomized design with three replications. The treatments include three concentrations of sodium alginate (1.5\%, 2.5\%, and 3.5\%), two ion exchange times (20 and 30 min), and two artificial seed germination media (hormone-free MS and MS supplemented with zeatin riboside and L-proline). Germination percentage and number of days needed until the beginning of germination were studied. The highest percentage of artificial seed germination was obtained when 2.5\% sodium alginate was used for 30 min (ion exchange time) and when the seeds were placed on the MS germination medium supplemented with zeatin riboside and L-proline. The results of the analysis of variance in the temporary immersion bioreactor system showed that the main effects observed on the seedling growth were associated with different growth hormones in culture media and the number of feeding cycles. Experimental results also indicated that the total protein analyses of zygotic seedlings and seedlings originating from the synthetic seeds showed no statistically significant differences between these samples.},
	language = {en},
	number = {22},
	urldate = {2022-12-02},
	journal = {Plants},
	author = {Aghbolaghi, Masoumeh Asadi and Dedicova, Beata and Sharifzadeh, Farzad and Omidi, Mansoor and Egertsdotter, Ulrika},
	month = jan,
	year = {2022},
	note = {Number: 22
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {in vitro cultures, protein analyses, somatic embryogenesis},
	pages = {3122},
}

This study was conducted to develop the protocol for artificial seed production of Stipagrostis pennata (Trin.) De Winter via somatic embryo encapsulation as well as test a temporary bioreactor system for germination and seedling growth. Embryogenic calli were encapsulated using sodium alginate and calcium chloride and then sowed in the Murashige and Skoog (MS) germination medium in in vitro cultures. The experiments were conducted as a factorial based on a completely randomized design with three replications. The treatments include three concentrations of sodium alginate (1.5%, 2.5%, and 3.5%), two ion exchange times (20 and 30 min), and two artificial seed germination media (hormone-free MS and MS supplemented with zeatin riboside and L-proline). Germination percentage and number of days needed until the beginning of germination were studied. The highest percentage of artificial seed germination was obtained when 2.5% sodium alginate was used for 30 min (ion exchange time) and when the seeds were placed on the MS germination medium supplemented with zeatin riboside and L-proline. The results of the analysis of variance in the temporary immersion bioreactor system showed that the main effects observed on the seedling growth were associated with different growth hormones in culture media and the number of feeding cycles. Experimental results also indicated that the total protein analyses of zygotic seedlings and seedlings originating from the synthetic seeds showed no statistically significant differences between these samples.

@article{mehra_hydraulic_2022,
	title = {Hydraulic flux–responsive hormone redistribution determines root branching},
	volume = {378},
	url = {https://www.science.org/doi/10.1126/science.add3771},
	doi = {10.1126/science.add3771},
	abstract = {Plant roots exhibit plasticity in their branching patterns to forage efficiently for heterogeneously distributed resources, such as soil water. The xerobranching response represses lateral root formation when roots lose contact with water. Here, we show that xerobranching is regulated by radial movement of the phloem-derived hormone abscisic acid, which disrupts intercellular communication between inner and outer cell layers through plasmodesmata. Closure of these intercellular pores disrupts the inward movement of the hormone signal auxin, blocking lateral root branching. Once root tips regain contact with moisture, the abscisic acid response rapidly attenuates. Our study reveals how roots adapt their branching pattern to heterogeneous soil water conditions by linking changes in hydraulic flux with dynamic hormone redistribution.},
	number = {6621},
	urldate = {2022-11-24},
	journal = {Science},
	author = {Mehra, Poonam and Pandey, Bipin K. and Melebari, Dalia and Banda, Jason and Leftley, Nicola and Couvreur, Valentin and Rowe, James and Anfang, Moran and De Gernier, Hugues and Morris, Emily and Sturrock, Craig J. and Mooney, Sacha J. and Swarup, Ranjan and Faulkner, Christine and Beeckman, Tom and Bhalerao, Rishikesh P. and Shani, Eilon and Jones, Alexander M. and Dodd, Ian C. and Sharp, Robert E. and Sadanandom, Ari and Draye, Xavier and Bennett, Malcolm J.},
	month = nov,
	year = {2022},
	note = {Publisher: American Association for the Advancement of Science},
	pages = {762--768},
}

Plant roots exhibit plasticity in their branching patterns to forage efficiently for heterogeneously distributed resources, such as soil water. The xerobranching response represses lateral root formation when roots lose contact with water. Here, we show that xerobranching is regulated by radial movement of the phloem-derived hormone abscisic acid, which disrupts intercellular communication between inner and outer cell layers through plasmodesmata. Closure of these intercellular pores disrupts the inward movement of the hormone signal auxin, blocking lateral root branching. Once root tips regain contact with moisture, the abscisic acid response rapidly attenuates. Our study reveals how roots adapt their branching pattern to heterogeneous soil water conditions by linking changes in hydraulic flux with dynamic hormone redistribution.

@article{sun_fiona1-mediated_2022,
	title = {{FIONA1}-mediated methylation of the 3’{UTR} of {FLC} affects {FLC} transcript levels and flowering in {Arabidopsis}},
	volume = {18},
	issn = {1553-7404},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010386},
	doi = {10.1371/journal.pgen.1010386},
	abstract = {Adenosine bases of RNA can be transiently modified by the deposition of a methyl-group to form N6-methyladenosine (m6A). This adenosine-methylation is an ancient process and the enzymes involved are evolutionary highly conserved. A genetic screen designed to identify suppressors of late flowering transgenic Arabidopsis plants overexpressing the miP1a microProtein yielded a new allele of the FIONA1 (FIO1) m6A-methyltransferase. To characterize the early flowering phenotype of fio1 mutant plants we employed an integrative approach of mRNA-seq, Nanopore direct RNA-sequencing and meRIP-seq to identify differentially expressed transcripts as well as differentially methylated RNAs. We provide evidence that FIO1 is the elusive methyltransferase responsible for the 3’-end methylation of the FLOWERING LOCUS C (FLC) transcript. Furthermore, our genetic and biochemical data suggest that 3’-methylation stabilizes FLC mRNAs and non-methylated FLC is a target for rapid degradation.},
	language = {en},
	number = {9},
	urldate = {2022-11-30},
	journal = {PLOS Genetics},
	author = {Sun, Bin and Bhati, Kaushal Kumar and Song, Peizhe and Edwards, Ashleigh and Petri, Louise and Kruusvee, Valdeko and Blaakmeer, Anko and Dolde, Ulla and Rodrigues, Vandasue and Straub, Daniel and Yang, Junbo and Jia, Guifang and Wenkel, Stephan},
	month = sep,
	year = {2022},
	keywords = {Arabidopsis thaliana, Flowering plants, Gene expression, Leaves, Messenger RNA, Methylation, Phenotypes, RNA sequencing},
	pages = {e1010386},
}

Adenosine bases of RNA can be transiently modified by the deposition of a methyl-group to form N6-methyladenosine (m6A). This adenosine-methylation is an ancient process and the enzymes involved are evolutionary highly conserved. A genetic screen designed to identify suppressors of late flowering transgenic Arabidopsis plants overexpressing the miP1a microProtein yielded a new allele of the FIONA1 (FIO1) m6A-methyltransferase. To characterize the early flowering phenotype of fio1 mutant plants we employed an integrative approach of mRNA-seq, Nanopore direct RNA-sequencing and meRIP-seq to identify differentially expressed transcripts as well as differentially methylated RNAs. We provide evidence that FIO1 is the elusive methyltransferase responsible for the 3’-end methylation of the FLOWERING LOCUS C (FLC) transcript. Furthermore, our genetic and biochemical data suggest that 3’-methylation stabilizes FLC mRNAs and non-methylated FLC is a target for rapid degradation.

@article{kruusvee_microproteins_2022,
	title = {Microproteins — lost in translation},
	volume = {18},
	copyright = {2022 Springer Nature America, Inc.},
	issn = {1552-4469},
	url = {https://www.nature.com/articles/s41589-022-01007-5},
	doi = {10.1038/s41589-022-01007-5},
	abstract = {Microproteins can be generated by a shift in the reading frame during translation. A chemoproteomics approach led to the identification of MINAS-60 as an alternative microprotein that regulates the assembly of the pre-60S ribosome.},
	language = {en},
	number = {6},
	urldate = {2022-11-30},
	journal = {Nature Chemical Biology},
	author = {Kruusvee, Valdeko and Wenkel, Stephan},
	month = jun,
	year = {2022},
	keywords = {Nuclear organization, Proteins, Proteomics},
	pages = {581--582},
}

Microproteins can be generated by a shift in the reading frame during translation. A chemoproteomics approach led to the identification of MINAS-60 as an alternative microprotein that regulates the assembly of the pre-60S ribosome.