TY  - JOUR
A1  - Winck, Flavia Vischi
A1  - Arvidsson, Samuel Janne
A1  - Mauricio Riano-Pachon, Diego
A1  - Hempel, Sabrina
A1  - Koseska, Aneta
A1  - Nikoloski, Zoran
A1  - Urbina Gomez, David Alejandro
A1  - Rupprecht, Jens
A1  - Müller-Röber, Bernd
T1  - Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga chlamydomonas reinhardtii under carbon deprivation
JF  - PLoS one
N2  - The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas.
Y1  - 2013
U6  - https://doi.org/10.1371/journal.pone.0079909
SN  - 1932-6203
VL  - 8
IS  - 11
PB  - PLoS
CY  - San Fransisco
ER  - 
TY  - JOUR
A1  - Lucia Gomez-Porras, Judith
A1  - Mauricio Riano-Pachon, Diego
A1  - Benito, Begona
A1  - Haro, Rosario
A1  - Sklodowski, Kamil
A1  - Rodriguez-Navarro, Alonso
A1  - Dreyer, Ingo
T1  - Phylogenetic analysis of K+ transporters in bryophytes, lycophytes, and flowering plants indicates a specialization of vascular plants
JF  - Frontiers in plant science
N2  - As heritage from early evolution, potassium (K+) is absolutely necessary for all living cells. It plays significant roles as stabilizer in metabolism and is important for enzyme activation, stabilization of protein synthesis, and neutralization of negative charges on cellular molecules as proteins and nucleic acids. Land plants even enlarged this spectrum of K+ utilization after having gone ashore, despite the fact that K+ is far less available in their new oligotrophic habitats than in sea water. Inevitably, plant cells had to improve and to develop unique transport systems for K+ accumulation and distribution. In the past two decades a manifold of K+ transporters from flowering plants has been identified at the molecular level. The recently published genome of the fern ally Selaginella moellendorffii now helps in providing a better understanding on the molecular changes involved in the colonization of land and the development of the vasculature and the seeds. In this article we present an inventory of K+ transporters of this lycophyte and pigeonhole them together with their relatives from the moss Physcomitrella patens, the monocotyledon Oryza sativa, and two dicotyledonous species, the herbaceous plant Arabidopsis thaliana, and the tree Populus trichocarpa. Interestingly, the transition of green plants from an aqueous to a dry environment coincides with a dramatic reduction in the diversity of voltage-gated potassium channels followed by a diversification on the basis of one surviving K+ channel class. The first appearance of K+ release (K-out) channels in S. moellendorffii that were shown in Arabidopsis to be involved in xylem loading and guard cell closure coincides with the specialization of vascular plants and may indicate an important adaptive step.
KW  - potassium
KW  - transport
KW  - channel
KW  - voltage-dependent
KW  - voltage-independent
KW  - high-affinity
KW  - Selaginella
Y1  - 2012
U6  - https://doi.org/10.3389/fpls.2012.00167
SN  - 1664-462X
VL  - 3
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Banks, Jo Ann
A1  - Nishiyama, Tomoaki
A1  - Hasebe, Mitsuyasu
A1  - Bowman, John L.
A1  - Gribskov, Michael
A1  - dePamphilis, Claude
A1  - Albert, Victor A.
A1  - Aono, Naoki
A1  - Aoyama, Tsuyoshi
A1  - Ambrose, Barbara A.
A1  - Ashton, Neil W.
A1  - Axtell, Michael J.
A1  - Barker, Elizabeth
A1  - Barker, Michael S.
A1  - Bennetzen, Jeffrey L.
A1  - Bonawitz, Nicholas D.
A1  - Chapple, Clint
A1  - Cheng, Chaoyang
A1  - Correa, Luiz Gustavo Guedes
A1  - Dacre, Michael
A1  - DeBarry, Jeremy
A1  - Dreyer, Ingo
A1  - Elias, Marek
A1  - Engstrom, Eric M.
A1  - Estelle, Mark
A1  - Feng, Liang
A1  - Finet, Cedric
A1  - Floyd, Sandra K.
A1  - Frommer, Wolf B.
A1  - Fujita, Tomomichi
A1  - Gramzow, Lydia
A1  - Gutensohn, Michael
A1  - Harholt, Jesper
A1  - Hattori, Mitsuru
A1  - Heyl, Alexander
A1  - Hirai, Tadayoshi
A1  - Hiwatashi, Yuji
A1  - Ishikawa, Masaki
A1  - Iwata, Mineko
A1  - Karol, Kenneth G.
A1  - Koehler, Barbara
A1  - Kolukisaoglu, Uener
A1  - Kubo, Minoru
A1  - Kurata, Tetsuya
A1  - Lalonde, Sylvie
A1  - Li, Kejie
A1  - Li, Ying
A1  - Litt, Amy
A1  - Lyons, Eric
A1  - Manning, Gerard
A1  - Maruyama, Takeshi
A1  - Michael, Todd P.
A1  - Mikami, Koji
A1  - Miyazaki, Saori
A1  - Morinaga, Shin-ichi
A1  - Murata, Takashi
A1  - Müller-Röber, Bernd
A1  - Nelson, David R.
A1  - Obara, Mari
A1  - Oguri, Yasuko
A1  - Olmstead, Richard G.
A1  - Onodera, Naoko
A1  - Petersen, Bent Larsen
A1  - Pils, Birgit
A1  - Prigge, Michael
A1  - Rensing, Stefan A.
A1  - Mauricio Riano-Pachon, Diego
A1  - Roberts, Alison W.
A1  - Sato, Yoshikatsu
A1  - Scheller, Henrik Vibe
A1  - Schulz, Burkhard
A1  - Schulz, Christian
A1  - Shakirov, Eugene V.
A1  - Shibagaki, Nakako
A1  - Shinohara, Naoki
A1  - Shippen, Dorothy E.
A1  - Sorensen, Iben
A1  - Sotooka, Ryo
A1  - Sugimoto, Nagisa
A1  - Sugita, Mamoru
A1  - Sumikawa, Naomi
A1  - Tanurdzic, Milos
A1  - Theissen, Guenter
A1  - Ulvskov, Peter
A1  - Wakazuki, Sachiko
A1  - Weng, Jing-Ke
A1  - Willats, William W. G. T.
A1  - Wipf, Daniel
A1  - Wolf, Paul G.
A1  - Yang, Lixing
A1  - Zimmer, Andreas D.
A1  - Zhu, Qihui
A1  - Mitros, Therese
A1  - Hellsten, Uffe
A1  - Loque, Dominique
A1  - Otillar, Robert
A1  - Salamov, Asaf
A1  - Schmutz, Jeremy
A1  - Shapiro, Harris
A1  - Lindquist, Erika
A1  - Lucas, Susan
A1  - Rokhsar, Daniel
A1  - Grigoriev, Igor V.
T1  - The selaginella genome identifies genetic changes associated with the evolution of vascular plants
JF  - Science
N2  - Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
Y1  - 2011
U6  - https://doi.org/10.1126/science.1203810
SN  - 0036-8075
VL  - 332
IS  - 6032
SP  - 960
EP  - 963
PB  - American Assoc. for the Advancement of Science
CY  - Washington
ER  -