An international research team investigated the genetic regulation of stem cell division in plant stems. During their investigations, they revealed that the key gene coordinating stem cells, WOX4, is controlled by the vital plant hormone auxin via auxin response proteins. The results are valuable for both fundamental biology and ecology. Since the studied mechanism allows controlling wood formation it could help to solve economic and environmental problems. The research has been published in the journal Nature Communications.

Scientists from the Centre for Organismal Studies (Germany), Gregor Mendel Institute (Austria), Institute of Cytology and Genetics (Russia), Novosibirsk State University (Russia), Wageningen University (Netherlands) and Institute for Plant Molecular and Cellular Biology, Polytechnic University of Valencia (Spain) showed a key role of auxin response regulatory proteins in the cambium (the stem cell niche responsible for wood formation, and also for specified spatial coordination features of gene activity.
Although an influence of auxin on the activity of WOX4 was known before, the exact mechanism was unclear. In this work, the authors demonstrated a direct regulation of WOX4 by auxin signaling factors.

Due to the strong focus on individual cell types, our analysis represents an important milestone for our research on cambium regulation. We more and more understand the exciting complexity of the regulatory network important for a very dynamic growth process which produce a large part of the biomass present on this planet,” said Thomas Greb professor of the Heidelberg University Centre for Organismal Studies and principal investigator of this study.

The amazing cambium and the great auxin

The cambium mediates wood formation which represents a large proportion of terrestrial biomass. The cambium is unique due to producing two different tissues at the same time — xylem also known as wood and phloem — in a bidirectional manner.

The xylem transports water together with dissolved nutrients and the phloem transports sugars essential for growth and development of cells. «Adult» vascular tissues are formed by dead cells and grow constantly in volume due to divisions of stem cells sitting in the cambium. It is important that xylem and phloem are not only produced during the embryonic period but throughout the plant life cycle. When the cambium «dies», so does the stem.

Scientists managed to study wood formation mechanisms in model plant Arabidopsis thaliana, the weed that doesn’t form thick wood itself. Intriguing, but Arabidopsis has all the genetic mechanisms required for wood formation. Thus, all the advantages of the model plant — a small size, a short life cycle and well-annotated genome – are used to investigate the complicated mechanism.

It was shown on Arabidopsis that a small molecule auxin is a King among plant hormones. It’s responsible for a huge amount of different jobs — following the sunlight by plants, responding to gravity, as well as controlling development of all plant organs, including embryos, roots, leaves and stems… Read more on EurekAlert

Plants sacrifice their newborn cells of the root tip in order to survive cold temperature conditions and retain their own ‘stem cells’
An international research team from Novosibirsk State University (NSU), the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), and the National University of Singapore have identified and analyzed the mechanism enabling plants to adapt to cold temperatures. This breakthrough was announced by NSU’s Computational Transcriptomic and Evolutionary Bioinformatics Laboratory (LCTEB)
It turns out that plants sacrifice their newborn cells of the root tip in order to survive cold temperature conditions and retain their own ‘stem cells.’ The study was published recently in Cell journal

Victoria Mironova, Ph.D. in Biology, the Head of LCTEB at NSU, Chief of the Sector for System Biology of Plant Morphogenesis at RAS Institute of Cytology and Genetics of Siberian Branch, commented.

“”Only a few stem cell daughters die under the chilling stress with the lifespan of these cells being very short also at normal conditions, whereas in contrast other tissues stay untouched

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MOSCOW, March 3. /TASS/ An international research team from Russia, Germany, and the USA have collected and analyzed data on how the plant hormone auxin influences the development of plants, the Computational Transcriptomic and Evolutionary Bioinformatics Laboratory at Novosibirsk State University (NSU) reported. In their study, the biologists used data both from experiments and from mathematical modeling. Such research, which enhances the understanding plants’ biochemistry will fine-tune the development of plants to the needs of people.

Victoria Mironova, the first author of the review published recently in the journal Trends in Plant Science, and Head of Computational Transcriptomic and Evolutionary Bioinformatics Laboratory at NSU, Head of Sector for Systems biology of plant morphogenesis at the Institute of Cytology and Genetics of RAS.:

In our work, we have revised an intricate regulatory action network of one of the most important plant hormones, auxin; the formula which describes how on a molecular level, auxin controls the activity of genes crucial for the development of seeds, separate parts of a plant (roots and stems) and of a plant as a whole(Read more on TASS … )

1. As a result of a search and a functional annotation of short regulatory sequences associated with auxin response, we predicted new regulatory elements involved in auxin responsiveness. The results are published in Journal of Bioinformatics and Computational Biology (Zemlyanskaya et al., 2016) and reported on the conference «Auxin-2016».
2. Based on the quantitative phenotyping of wheat leaf pubescence in various cultivars and lines , a model of the genetic control of leaf pubescence by the genes Hl1, Hl3 and Hl2aesp was proposed. The results are published in Euphytica (Doroshkov et al., 2016).
3. We developed a new approach for an integrated analysis of whole-genome annotations of chromatin states and ChIP-Seq data, which enables the complex characterization of mechanisms for the regulation of gene expression. We used this approach to show that the combination of chromatin characteristics and nucleotide context in EIN3 binding regions could determine various modes of EIN3-dependent regulation of the primary transcriptional response to ethylene. The results are published in Frontiers in Plant Science (Zemlyanskaya et al., 2017).
4. We showed that the origin of subtelomeric heterochromatin blocks in rye is associated with both the activity of mobile elements and the spread of tandem repeats. The results are published in BMC Genomics (Evtushenko et al., 2016).
5. The consistency of the transcriptional response to auxin in various groups of arabidopsis genes was assessed. A phenomenon of fold-specific gene expression in response to auxin was revealed and analysed (Omelyanchuk et al., Sci. Rep., under review).

1. The structural features of auxin responsive elements were detected. The developed bioinformatical method is uniform and can be used for the study of other molecular-genetics processes with complex regulation.
2. The evolution of auxin biosynthesis pathway in plants revisited. Stoneworts Klebsormidium flaccidum are the only algae in which the homologs of higher plants’ auxin biosynthesis enzymes were found. This fact testified in favor of the hypothesis of vertical inheritance of auxin biosynthesis pathway from multicellular algae to the higher land plants. In collaboration colleagues from ICG we performed comparative analysis of algae, moss and higher plants genomes. Based on the results of the reconstruction of three-dimensional structure of proteins, analysis of domain structure and detailed phylogenetic analysis it was shown that the homologs of auxin biosynthesis enzymes, previously reported in K. flaccidum, are not the ones. The obtained results testify in favor of the hypothesis of horizontal transfer of the auxin biosynthesis genes during the colonization of land by plants. The work was published in Trends in plant science, 2015.
3. The 3D map of PIN1 expression domain in the stem cell nishe of A. thaliana root meristem was described.
In collaboration with Klaus Palme’ lab we perform systems analysis of auxin distribution in the plant root
4. A number of bioinformatical methods and approaches were developed for biological data analysis. In collaboration with experimental biologists, the lab members were developed the methods for transcriptome analysis, SNP distribution, non-coding RNA , 3D chromatin organization. We developed the algorithms and methods of bioinformatic analysis of whole genome markings and its link to the known annotation of genes structure, including proximal and distal parts of promoter, exons and introns of 5’-untranslated region, etc. and methods for prediction of gene translation elongation efficiency (Sokolov et al., Journal of Integrative Bioinformatics, 2015)