bims-plasge 2019-06-02 papers

Issue of 2019–06–02
two papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Plant Physiol. 2019 May 28. pii: pp.00421.2019. [Epub ahead of print]

Extensive Post-Transcriptional Regulation of Nuclear Gene Expression by Plastid Retrograde Signals.

Guo-Zhang Wu, Etienne H Meyer, Si Wu, Ralph Bock.

Retrograde signals emanate from the DNA-containing cell organelles (plastids and mitochondria) and control the expression of a large number of nuclear genes in response to environmental and developmental cues. Previous studies on retrograde signaling have mainly analyzed the regulation of nuclear gene expression at the transcript level. To determine the contribution of translational and post-translational regulation to plastid retrograde signaling, we combined label-free proteomics with transcriptomic analysis of Arabidopsis (Arabidopsis thaliana) seedlings and studied their response to interference with the plastid gene expression (PGE) pathway of retrograde signaling. By comparing the proteomes of the genomes uncoupled 1 (gun1) and gun5 mutants with wild-type , we show that GUN1 is critical in the maintenance of plastid protein homeostasis (proteostasis) when plastid translation is blocked. Combining transcriptomic and proteomic analyses of wild-type and gun1, we identified 181 highly translationally or post-translationally regulated (HiToP) genes. We demonstrate that HiToP photosynthesis-associated nuclear genes (PhANGs) are largely regulated by translational repression, while HiToP ribosomal protein genes are regulated post-translationally - likely at the level of protein stability without the involvement of GUN1. Our findings suggest distinct post-transcriptional control mechanisms of nuclear gene expression in response to plastid-derived retrograde signals. They also reveal a role for GUN1 in the translational regulation of several PhANGs, and highlight extensive post-translational regulation that does not necessitate GUN1. This study advances our understanding of the molecular mechanisms underlying intracellular communication, and provides new insight into cellular responses to impaired plastid protein biosynthesis.

DOI: https://doi.org/10.1104/pp.19.00421

Mol Phylogenet Evol. 2019 May 27. pii: S1055-7903(18)30660-2. [Epub ahead of print]

Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes.

Deise J P Gonçalves, Beryl B Simpson, Edgardo M Ortiz, Gustavo H Shimizu, Robert K Jansen.

The current classification of angiosperms is based primarily on concatenated plastid markers and maximum likelihood (ML) inference. This approach has been justified by the assumption that plastid DNA (ptDNA) is inherited as a single locus and that its individual genes produce congruent trees. However, structural and functional characteristics of ptDNA suggest that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces. To examine this idea, we produced new complete plastid genome (plastome) sequences of 27 species and combined these data with publicly available sequences to produce a final dataset that includes 78 plastid genes for 89 species of rosids and five outgroups. We used four data matrices (i.e., gene, exon, codon-aligned, and amino acid) to infer species and gene trees using ML and multispecies coalescent (MSC) methods. Rosids include about one third of all angiosperms and their two major clades, fabids and malvids, were recovered in almost all analyses. However, we detected incongruence between species trees inferred with different matrices and methods and previously published plastid and nuclear phylogenies. We visualized and tested the significance of incongruence between gene trees and species trees. We then measured the distribution of phylogenetic signal across sites and genes supporting alternative placements of five controversial nodes at different taxonomic levels. Gene trees inferred with plastid data often disagree with species trees inferred using both ML (with unpartitioned or partitioned data) and MSC. Species trees inferred with both methods produced alternative topologies for a few taxa. Our results show that, in a phylogenetic context, plastid protein-coding genes may not be fully linked and behaving as a single locus. Furthermore, concatenated matrices may produce highly supported phylogenies that are discordant with individual gene trees. We also show that phylogenies inferred with MSC are accurate. We therefore emphasize the importance of considering variation in phylogenetic signal across plastid genes and the exploration of plastome data to increase accuracy of estimating relationships. We also support the use of MSC with plastome matrices in future phylogenomic investigations.

Keywords: alternative topologies; coalescence; gene trees; plastome; species trees; tree space

DOI: https://doi.org/10.1016/j.ympev.2019.05.022